An early goal from Callum Connolly settled a contest that saw the conditions dictate the level of quality on display.
Ronan Curtis struck the woodwork and Sean Raggett’s header was cleared from the line, but the Blues were unable to find a leveller.
Kenny Jackett had to make a late change to his line-up, with Ellis Harrison originally included in the side.
But he was still feeling his dead leg in the warm-up and was switched for Oli Hawkins, which in turn opened up a place on the bench for Gareth Evans.
There were two other changes from the side that dramatically beat Exeter to reach the Leasing.com Trophy earlier in the week.
John Marquis was rewarded for his last-gasp winner, while James Bolton came in at right-back, as Ben Close and Ross McCrorie dropped to the bench.
There was driving rain and hail before kick-off, although that had thankfully passed by the time the players emerged from the tunnel.
But there was still a strong wind blowing around Highbury and it was clearly making life difficult for both sides.
Pompey were first to threaten and Lewie Coyle slid in to clear before Curtis could meet a low Marquis centre.
It was the hosts who broke the deadlock on 12 minutes, though, with Connolly left in too much space to nod home after Alex Bass had parried away Danny Andrew’s cross.
There was soon some more sloppy play from the Blues to give away possession in the middle of the pitch.
Barrie McKay collected the ball and laid it off for the rampaging Wes Burns, who could only drill past the post.
Pompey then came close to a wind-assisted leveller when Curtis’ wide free-kick drifted towards goal and rattled the crossbar.
A couple of Paul Coutts corners caused problems at the other end, with Christian Burgess nodding the first behind and Bass then punching the second in the air before catching the ball.
The keeper then made sure he got right behind a long-range effort from Paddy Madden to gather cleanly.
There were not an abundance of clear-cut chances, with the conditions certainly having an effect on the quality on show.
But Fleetwood breathed a sigh of relief when Curtis beat Alex Cairns to Steve Seddon’s pass down the line and with the keeper stranded, the ball would not fall kindly for a grey-shirted player.
There was time for a booking for Harry Souttar just before the break, with the defender petulantly throwing the ball away to stop the visitors from taking a throw.
Fleetwood Town 1
There was no let-up in the wind by the time the action restarted, with Tom Naylor having to gather some paperwork from the visitors’ dug-out that had blown onto the pitch.
It was certainly not helping the game as a spectacle, with any kind of rhythm absent from both teams’ play.
There was a shot from outside the box by Marquis on 55 minutes, although he could only scuff it wide.
Jackett soon made a double switch to try to improve Pompey’s fortunes, as McCrorie and Ryan Williams replaced James Bolton and Hawkins.
And when McCrorie played a deep pass into the box, the ball was volleyed narrowly past the post by the lively Curtis.
That came just a few seconds after Bass had got down to his right to make a regulation stop from Paddy Madden’s drive.
He had to make a smarter stop to deny Burns, diving the opposite way to parry clear a shot that swerved in the wind.
Pompey were being frustrated by their well-drilled opponents, although a leveller almost arrived on 73 minutes.
Curtis was the provider of a dangerous corner that was met by Raggett’s firm header, which was cleared from the line by Coyle.
Seddon then had an attempt from inside the box blocked, as Fleetwood continued to stand firm at the back.
There might have been a goal at the other end when Curtis’ cross-field pass was intercepted, but Josh Morris drilled wide after racing clear.
Raggett was deployed as an emergency striker in an attempt to find an equaliser, but tempers were getting frayed and the referee had to deal with some pushing and shoving.
When that finally calmed down, the Cod Army held on through five minutes of stoppage-time to claim all three points.
Fleetwood (4-2-3-1): Cairns; Coyle, Souttar, Gibson, Andrew; Coutts (c), Connolly (Sowerby 81); Burns, Whelan, McKay (Morris 76); Madden (Saunders 90+4)
Goals: Connolly 12
Booked: Souttar, Burns, Coutts
Subs not used: Crellin, Holgate, Thorvaldsson, Biggins
Pompey (4-2-3-1): Bass; Bolton (McCrorie 56), Burgess, Raggett, Seddon; McGeehan, Naylor (c); Harness, Marquis, Curtis; Hawkins (Williams 56)
Booked: Seddon, Naylor
Subs not used: MacGillivray, Whatmough, Haunstrup, Close, Evans
Referee: Matt Donohue
Attendance: 3,370 (747 away fans)