It looked like Conor Chaplin would be the hero for a second game in succession when he headed the Blues level early in the second half.
Adam Armstrong had earlier scored for Rovers and the same player struck again to deflate a large home crowd.
Lewis Travis saw red for the visitors in stoppage-time, but they held on to boost their automatic promotion hopes.
Kenny Jackett made three changes from the side that dramatically beat MK Dons at the weekend.
Chaplin was rewarded for his stoppage-time winner with a start, along with Jamal Lowe and – returning from suspension – Christian Burgess.
Matty Kennedy, Connor Ronan and Oli Hawkins were the men to make way, with the trio dropping to the bench.
There was an early warning for the hosts when Ben Close lost possession to Jack Payne. He found Bradley Dack, only for Luke McGee to come to the rescue with a smart stop.
Pompey tried to make an impact at the other end and Dion Donohue’s volley was kept out by David Raya, while the keeper then prevented Chaplin’s cross from reaching an unmarked Brett Pitman.
It was the visitors looking more dangerous, though, and when Charlie Mulgrew whipped a free-kick into the box, Paul Downing glanced just wide.
And the deadlock was broken on 21 minutes, as Mulgrew flicked on Richie Smallwood’s cross and Armstrong turned the ball home.
The Blues picked up the pace in the search for an equaliser, with Chaplin and Close both seeing efforts blocked in quick succession.
Ryan Nyambe then made a vital header when Nathan Thompson tried to float a pass to Close in the Rovers box.
Pitman had the hosts’ best chance on 32 minutes, as he wriggled into a shooting position, with Raya getting down to save his angled drive.
Pompey kept plugging away, but Gareth Evans ballooned over when Donohue picked him out in the area.
Pitman also lacked his usual composure by firing wide, while Lowe was then off target with a diving header.
But the Blues finished the half strongly and Raya got down to save when Evans met another dangerous Donohue delivery with a deft flick.
Anton Walkes also had a decent effort in stoppage-time and there were gasps as the ball curled agonisingly past the post.
Blackburn Rovers 1
The hosts had improved as the first half progressed and found themselves level within five minutes of the restart.
Donohue sent a cross in from the left and Walkes did well to hook it back into the centre, where CHAPLIN was waiting to head home from close range.
They might have had another soon after when Raya came tearing from his box, but failed to collect the ball.
Pitman did gather it and steadied himself on the left side of the area, although he was unable to curl his shot on target.
Raya had collided with team-mate Nyambe in that incident and the defender received warm applause as he was stretched off towards a waiting ambulance.
McGee denied Dack at the other end, but the action had started to lull following a breathless start to the second half.
But Pompey injected life back into proceedings when Donohue’s cross was not properly dealt with and Close’s follow-up was deflected narrowly wide.
There was a sense of urgency at both ends of the pitch as the clock ticked down into the final 15 minutes.
Close did well to get down the right and centre the ball, with it being headed behind before Lowe could take advantage on the back post.
A seemingly innocuous cross from Armstrong then crept narrowly wide, as did Mulgrew’s deep free-kick moments later.
Chaplin was cheered off the pitch when Jackett decided to replace him with Hawkins for the final few minutes.
But the mood soon soured, as Rovers restored their advantage. Darragh Lenihan’s cross ricocheted off Matt Clarke and fell kindly for Armstrong to lash in his second of the night.
Hopes were raised by the display of seven additional minutes, while Travis’ red card for a late challenge on Thompson provided more cause for optimism.
Pompey threw men forward in a desperate search for another equaliser, but Blackburn held on to secure the spoils.
Pompey (4-4-2): McGee; Walkes, Burgess, Clarke, Donohue; Evans, Thompson, Close, Lowe (Kennedy 90+2); Chaplin (Hawkins 85), Pitman (c)
Goals: Chaplin 50
Subs not used: Bass, Deslandes, May, Ronan, Naismith
Blackburn (4-2-3-1): Raya; Nyambe (Lenihan 56), Downing, Mulgrew (c), Williams; Bennett, Smallwood; Payne (Travis 56), Dack, Armstrong; Samuel (Graham 82)
Goals: Armstrong 21, 87
Sent off: Travis
Subs not used: Leutwiler, Bell, Evans, Conway
Referee: Oliver Langford
Attendance: 18,152 (884 away fans)