Gareth Evans and Stuart O’Keefe were on target as Pompey cruised into the last 16 of the Checkatrade Trophy.
A small crowd were not treated to a chance-laden encounter against Northampton, but it was always the hosts who looked more likely to progress.
Evans completed an attractive passing counter-attack to open the scoring a few minutes before the interval.
O’Keefe doubled their lead in the second half and only some impressive saves from David Cornell prevented the margin of victory being even greater.
Kenny Jackett made three changes from the side that beat Plymouth in the league the previous week.
Christian Burgess returned from suspension to replace the injured Oliver Hawkins in defence, while the sidelined Kal Naismith made way for Curtis Main up front.
The other switch saw loanee O’Keefe recalled in the centre of the pitch, with Ben Close, who was nursing a knock, missing out.
A sparse attendance ensured there was an eerie atmosphere inside Fratton Park when the game got underway.
And the action on the pitch did little to warm the spirits of those fans who decided to spurn Christmas shopping to watch the contest.
There were a couple of half chances for the hosts, with O’Keefe’s volleyed effort flying over, while an audacious long-range free-kick from Christian Burgess landed on the roof of the net.
Neither side looked particularly threatening in the opening stages, however, as the game drifted along.
Main headed a difficult chance wide after rising above two defenders to meet Nathan Thompson’s cross.
Evans then drilled a low shot narrowly past the post, while Cornell – who previously had a loan spell at Fratton Park – just about beat Conor Chaplin to a loose ball.
The tie finally got going on 35 minutes, when Danny Rose slipped a fine pass through to Evans, who was denied by Cornell’s save.
Northampton had offered little at the other end, although Burgess made a timely challenge to dispossess Chris Long in the box.
And it was the Blues who broke the deadlock just before the break, courtesy of a fine passing move up the pitch.
Brandon Haunstrup released Evans, who in turn found Chaplin before bursting into the box to receive the ball back.
Chaplin dinked a cross into the centre, and EVANS was there to head home his first goal of the season.
Northampton Town 0
The advantage was almost doubled early in the second half, as Haunstrup delivered a dangerous low cross that Ash Taylor had to turn over his own crossbar.
But it then took a superb save from Luke McGee to stop the Cobblers from levelling, with the keeper diving to his right to stop Taylor from converting Lewis McGugan’s corner.
Cornell made his own decent stop when Main inventively flicked Rose’s centre towards the net, although the linesman had raised his flag for offside.
The lead did increase just before the hour mark, however, as Thompson cut the ball back for O’KEEFE to neatly steer into the bottom corner.
A third might have followed when Thompson stole back possession, but Evans’ effort from out wide flashed past the post.
Jackett made his first switch on 69 minutes, with Drew Talbot given a chance to impress in place of Haunstrup at left-back.
Evans and Chaplin were off target with shots, as the Blues tried to wrap the tie up with plenty of time to spare.
Main then saw an attempt roll agonisingly wide following good work from Rose and Chaplin to tee him up.
And Cornell made a string of fine saves to limit the damage late on, denying Main, Evans and Chaplin in quick succession.
Pompey (4-2-3-1): McGee; Thompson, Burgess, Clarke, Haunstrup (Talbot 69); O’Keefe, Rose; Evans (c), Chaplin, Lowe (Kennedy 88); Main
Goals: Evans 41, O’Keefe 58
Subs not used: Bass, Casey, May, Bennett, Lethbridge
Northampton (4-4-2): Cornell; Moloney, Barnett, Taylor, Buchanan; Hoskins (Bowditch 63), Poole (Waters 78), McGugan, Crooks; Richards (c), Long (Foley 46)
Subs not used: Coddington, Smith, McGivern, Kasim
Referee: Tom Nield
Attendance: 1,780 (128 away fans)
Pompey boosted their chances of a qualifying for the Checkatrade Trophy knockout stages with victory over Crawley at a sparsely-populated Fratton Park.
Matt Clarke opened the scoring with the type of goal you would not normally associate with a defender.
His stand-in back-line partner Oliver Hawkins then doubled the lead, only for Moussa Sanoh to pull one back after the break.
But Stuart O’Keefe added a third for the hosts to wrap the points up and move the Blues to the top of Southern Group A.
Kenny Jackett made six changes from the side that were beaten at home by Oldham at the weekend.
Gareth Evans returned to skipper the side at right-back, while Danny Rose and Adam May were recalled in midfield.
Curtis Main led the line and there were also starts in attacking roles for both Kal Naismith and Kyle Bennett.
Pompey’s defensive injury crisis meant that striker Hawkins had to continue partnering Clarke in the centre of defence.
It was a fairly quiet start to proceedings, with neither side managing to create any clear-cut openings.
Bennett had an effort blocked, while Rose’s diagonal pass was just too heavy for Main, allowing Red Devils keeper Yusuf Mersin to claim.
Main did go close on 12 minutes, though, collecting Naismith’s through ball and fizzing an angled drive just past the post.
Crawley then forced Luke McGee into action for the first time midway through the first half, with the keeper doing well to push behind Kaby Djalo’s fierce drive.
But it was the Blues who broke the deadlock on 30 minutes and it was an impressive goal from CLARKE.
He ran more than half the length of the pitch before feeding Main and was on hand to calmly convert when the striker’s shot was saved.
And his central defensive partner HAWKINS soon doubled the lead, slamming home the loose ball after Main’s header from a Naismith free-kick had been kept out by Mersin.
The visitors then missed an opportunity to reduce the deficit just before the break when Panutche Camara fired wide.
Crawley Town 0
The Red Devils made a bright start to the second half, but a couple of half-chances failed to test McGee.
Ibrahim Meite then took a heavy touch from Sanoh’s dangerous low delivery to waste another decent opening.
And when Sanoh crossed dangerously for a second time, the ball was just out of reach for both Meite and Camara, as the visitors continued to threaten.
The impressive Sanoh had a shot of his own just before the hour mark, but McGee was equal to his powerful effort.
Jackett made a double switch soon after, withdrawing May and Rose for Brandon Haunstrup and Jamal Lowe.
But it was Bennett who had a great chance to wrap the game up when he took the ball past Mersin, only to fire over with the goal gaping.
And Crawley immediately went down the other end to reduce their deficit, with Sanoh racing onto Camara’s flick and sliding past McGee.
But Bennett soon made up for his miss by providing the assist for Pompey’s third goal of the evening on 71 minutes.
He jinked his way into the box and teed-up O’KEEFE to slot home and open his scoring account for the club.
Bennett might have added a gloss to the scoreline late on when he was left unmarked to meet Lowe’s cross, but sent his header wide.
Pompey (4-2-3-1): McGee; Evans (c), Hawkins, Clarke, Donohue; May (Haunstrup 62), Rose (Lowe 62); O’Keefe (Close 87), Bennett, Naismith; Main
Goals: Clarke 30, Hawkins 34, O’Keefe 71
Subs not used: Bass, Talbot, Kennedy, Chaplin
Crawley (4-2-3-1): Mersin; Tajbakhsh (Lewis 76), McNerney, Yorwerth, Djalo (Smith 87); Payne, Bulman (c); Camara (Boldewijn 76), Clifford, Sanoh; Meite
Goals: Sanoh 65
Subs not used: Morris, Evina, Connolly, Lelan
Referee: Tim Robinson
Attendance: 1,527 (44 away fans)
Loan : Cardiff City – Portsmouth