Pompey suffered their first home defeat since March, as Rotherham left Fratton Park with all three points.
Jon Taylor netted the only goal during the first half of a televised contest that improved as it went on.
The Blues were much better after the break, but were unable to convert any of the numerous chances they carved out.
Kenny Jackett made four changes from the side that drew at Wigan the previous week.
He handed debuts to Stuart O’Keefe and Oliver Hawkins, while fellow deadline day signings Damien McCrory and Matty Kennedy had to be content with a place on the bench.
Matt Clarke returned from the groin injury that had kept him sidelined since pre-season and there was also a start for Conor Chaplin.
That saw a switch to a 3-4-1-2 system, with Brandon Haunstrup and Jamal Lowe occupying the wide roles, and skipper Brett Pitman playing behind Chaplin and Hawkins.
The rain was falling heavily when the game got underway and the action on the pitch was doing little to brighten the mood.
It was a fairly lethargic opening to proceedings, with both sides struggling to keep hold of the ball, perhaps hindered by the wet conditions.
The first chance fell for the hosts, though, and Pitman ran at the Rotherham defence, beat his man and fired narrowly over the bar.
But the Millers soon threatened themselves, with Michael Ihiekwe failing to find the target before O’Keefe bravely blocked Lee Frecklington’s effort.
Kieffer Moore than tried his luck from the edge of the box, but could not make a clean connection and the ball bobbled safely into Luke McGee’s arms.
There were not too many clear-cut openings, but the Blues did have opportunites to break the deadlock.
Haunstrup saw a shot deflected past the post after meeting Adam May’s delivery, while Hawkins’ long-range attempt only flew narrowly wide.
Instead it was Rotherham who took the lead on 36 minutes, as Taylor latched onto a ball down the right and lashed home a powerful strike.
Pompey immediately set about trying to find a leveller and Clarke failed to divert Chaplin’s corner on target.
A superb cross Haunstrup cross from wide on the left was then headed over by Lowe, as the hosts went in behind at the break.
Rotherham Untied 1
Jackett made a change of personnel and system for the start of the second half, with a return to four at the back.
Jack Whatmough and Chaplin both failed to emerge from the tunnel and were replaced by debutants Nathan Thompson and Kennedy.
And the latter made in instant impression with a cross that Millers keeper Richard O’Donnell could not get to.
The ball landed at the feet of Lowe at the far post and he took a touch before sending in a low drive that was deflected behind.
Pompey fans were baying for a penalty when Hawkins took a boot to the face on 57 minutes, although referee Gavin Ward was not interested.
There was then a lighter moment just past the mark, as Pitman and Kennedy both tried to keep the ball in play and the former ended up taking out the latter!
The hosts were looking much more dangerous than before the break and when a bandaged Hawkins met May’s free-kick, his header had to be cleared from the line by Darren Potter.
Jackett made a final throw of the dice on 70 minutes, with Hawkins given a generous ovation as he made way for Kal Naismith.
But the Scottish forward was getting patched up on the sidelines following a challenge with O’Donnell when the Blues came close to levelling on 79 minutes.
It was a dangerous low ball into the box from a slightly out-of-position Clarke, but a stretching Lowe could not quite make a connection at the far post.
Pompey poured forward in the closing stages, which were played out almost entirely in Rotherham’s half.
And the display of six additional minutes gave the Fratton faithful hope of salvaging something, but the visitors held on for victory.
Pompey (3-4-1-2): McGee; Burgess, Whatmough (Thompson 46), Clarke; Lowe, May, O’Keefe, Haunstrup; Pitman (c); Chaplin (Kennedy 46), Hawkins (Naismith 70)
Subs not used: Bass, McCrory, Close, Donohue
Rotherham (4-2-3-1): O’Donnell; Cummings, Ihiekwe, Wood, Purrington; Potter, Vaulks; Williams (Forde 54), Frecklington (c) (Towell 90+1), Taylor (Newell 85); Moore
Goals: Taylor 36
Booked: Potter, Purrington, Vaulks
Subs not used: Bilboe, Ajayi, Clarke-Harris, Ball
Referee: Gavin Ward
Loan : Cardiff City – Portsmouth
Pompey have signed Matty Kennedy from Cardiff on a season-long loan deal, subject to international clearance.
The Scottish winger becomes the fourth deadline day arrival at Fratton Park, following the captures of Oliver Hawkins, Stuart O’Keefe and Damien McCrory.
Blues boss Kenny Jackett said: “Matty’s a very skilful attacking midfielder with the great ability to go past players.
“He also has a good record of assists and will be able to provide for our strikers with quality crosses.
“He played against us in the Carabao Cup and produced an impressive performance, so I’m sure he’ll be a very effective player for us.”
Kennedy began his career with Kilmarnock and had a spell at Everton before signing for Cardiff in February 2015.
He appeared in three games for the Welsh outfit this season – including August’s cup clash – and has represented Scotland up to under-21 level.
Loan : Portsmouth – Colchester United
Nicke Kabamba has joined Colchester on loan until January.
The 24-year-old striker has made six appearances since joining Pompey from Hampton & Richmond in January.
Blues boss Kenny Jackett said: “In terms of League football he’s still very young.
“This move gives him the opportunity to play some senior games and continue his route towards the Pompey first team.”
Loan : Burton Albion – Portsmouth
Pompey have signed Damien McCrory on loan from Burton until January.
The 27-year-old Irishman is primarily a left-back, but can also be utilised in a more advanced position.
Blues boss Kenny Jackett said: “He’s an experienced player who provides competition for Brandon Haunstrup in that role.
“It’s a specialist position and we’ve been looking to bring someone in since Tareiq Holmes-Dennis’ unfortunate injury on the opening day.
“He’s won promotion from this division before and has also played in the Championship, so we’re delighted to bring him in on loan.”
McCrory started his career at Plymouth and enjoyed a successful stint with Dagenham before joining Burton in 2012.
He has made almost 200 appearances for the Brewers and represented Republic of Ireland at youth level.
Portsmouth Football Club can confirm that Michael Smith has left the club by mutual consent.
The striker netted 10 goals in his 37 appearances for the Blues after arriving – initially on loan – in February 2016.
Three of those came in League Two last term, with a crucial equaliser at Cheltenham that helped secure the title.
Smith also bagged a hat-trick at Yeovil in a 4-3 group stage defeat in the Checkatrade Trophy.
Michael Smith subsequently signed for Bury
Loan : Cardiff City – Portsmouth
Pompey have signed midfielder Stuart O’Keefe from Cardiff on a season-long loan, subject to international clearance.
The 26-year-old has previously helped Crystal Palace win promotion from the Championship and featured for them in the Premier League.
Blues boss Kenny Jackett said: “We’re very pleased to bring Stuart in for the rest of the season.
“He brings experience and aggression into our midfield and will complement the young ball-playing guys in that area of the pitch.”
O’Keefe progressed through the ranks at Southend before joining the Eagles and then arriving at Cardiff in 2015.
He has scored twice in 45 appearances for the Welsh club and appeared against Pompey in the Carabao Cup earlier this season.
Transfer : Dagenham & Redbridge – Portsmouth
Pompey have signed Oliver Hawkins from Dagenham & Redbridge.
The towering 25-year-old striker has arrived for an undisclosed fee and penned a three-year deal at Fratton Park.
Blues boss Kenny Jackett said: “We’re really pleased to get Oliver over the line and I’m looking forward to working with him.
“He’s someone I’ve watched for a long time and is capable of stepping out of non-league and doing well for us, complementing the players we’ve already got.
“He will obviously add some physicality to our squad. He holds the ball up and is a big threat in the box – in fact he’s useful in both boxes.”
Hawkins started his career with North Greenford United and enjoyed prolific spells with Hillingdon Borough, Northwood and Hemel Hempstead before signing for Dagenham in January 2016.
He netted 18 goals for the Daggers in the National League last season, including hat-tricks against Wrexham and Solihull.
Portsmouth Football Club can confirm that Carl Baker has left the club by mutual consent.
The 34-year-old midfielder arrived at Fratton Park in June 2016 and netted nine times in 50 appearances during his time on the south coast.
He scored crucial goals against the likes of Carlisle, Cambridge and Mansfield to help the Blues secure the League Two title last season.
Baker also appeared four times this term, featuring in the games against Rochdale, Cardiff, Oxford and Fulham under-21s.
Carl Baker subsequently signed for Atlético de Kolkata (India)
Transfer : Portsmouth – Coventry City
Tom Davies has signed for Coventry for an undisclosed fee.
The 25-year-old centre-back will join former Pompey team-mates Michael Doyle and Liam O’Brien at the Ricoh Arena.
He joined the Blues from Accrington last summer and made a total of 16 first team appearances during his time on the south coast.
Davies only featured once this term, however, partnering Jack Whatmough in defence for the Checkatrade Trophy draw with Fulham under-21s.