It was former Blues striker John Akinde who grabbed the only goal of the game from the penalty spot late in the first half.
The visitors improved after the interval and Adam McGurk went closest in their ultimately unsuccessful attempt to find an equaliser.
Paul Cook made three changes from the side that drew with Yeovil at the weekend.
Marc McNulty came in up front, with Michael Smith dropping to the bench, while there were also starts for Matt Clarke and McGurk in place of the suspended Christian Burgess and injured Gareth Evans.
Pompey struggled to deal with Barnet’s physical style in the first half and lacked any real fluidity going forward.
There were no real scoring chances in the opening stages and the only noteworthy moment was an early substitution.
Gary Roberts hurt his hamstring in a challenge after just eight minutes and had to be replaced by Kal Naismith.
The first opportunity fell to the hosts, with Ryan Fulton just about preventing a Sam Muggleton corner from creeping in at the near post.
Akinde then raced onto a long ball forward, but – under pressure from Adam Webster – could only hit a tame effort straight at Fulton.
But excitement was thin on the ground in a largely attritional and niggly encounter that failed to spark.
Both sides realised that shots from long-range might be the best way to break the deadlock and swerving efforts from Naismith and Mark Randall were just about dealt with by the respective keepers.
Instead, the opening goal came from the penalty mark and arrived after Ben Davies’ gained too many yards from a throw to see possession overturned.
The ball was launched into the Blues box, where Webster was adjudged to have tripped Akinde.
Referee Philip Gibbs pointed straight to the spot and it was Akinde stepped up to coolly slot the ball into the bottom corner.
That seemed to jolt Pompey into life and Bondz N’Gala made a vital block to deny McNulty before Jamie Stephens gathered McGurk’s long-range strike at the second attempt.
The visitors made a sloppy start to the second half, but Mathew Stevens was unable to capitalize on some poor defending.
They almost drew level moments later, however, with McGurk rising above his marker to meet Davies’ cross and draw a fingertip save from Stephens.
A deep free-kick from Naismith then somehow evaded everyone as it curled frustratingly out of play.
Cook made his second switch on the hour mark – and it was an attacking one as Ben Close made way for Smith.
But it was Naismith who should have leveled moments later, firing over the bar after being picked out by McNulty’s cut-back.
Clarke was next to go close on 66 minutes when he met Naismith’s free-kick from the left and saw his header saved by Stephens.
Pompey were looking much more of a threat now and it took a last-gasp clearance by Michael Nelson to get Davies’ low cross to safety.
Cook made his final throw of the dice on 78 minutes, bringing on Conor Chaplin in place of McNulty.
He was soon into the action after being bundled over by Tom Champion, only to see his free-kick punched clear by Stephens.
The Blues kept pushing forward in the closing stages, but their large travelling support – who made up more than half of the total attendance – were not to be rewarded.
Barnet (4-2-3-1): Stephens; Pearson, N’Gala, Nelson, Muggleton; Randall (Vilhete 62), Champion; Yiadom (c), Stevens (Togwell 52), Weston; Akinde (Sesay 84)
Goals: Akinde 41 (pen)
Booked: Champion, Randall, Yiadom, Muggleton
Subs not used: McKenzie-Lyle, Shomotun, Gambin, Hackett
Pompey (4-2-3-1): Fulton; Davies, Webster, Clarke, Stevens; Close (Smith 60), Doyle (c); McGurk, Roberts (Naismith 8), Bennett; McNulty (Chaplin 78)
Subs not used: Bass, Freeman, Barton, Hollands
Referee: Philip Gibbs
Attendance: 2,557 (1,330 Pompey fans)