Christian Burgess’ first-half striker delivered the Blues a 1-0 success against the basement side at the University of Bolton Stadium.
Kenny Jackett’s men were put under constant siege in the second half but failed to be breached and remain outside the play-offs only on goal difference.
Pompey made one change from last week’s victory over AFC Wimbledon, with John Marquis replacing Andy Cannon.
Fit-again Ryan Williams returned to the bench, which meant Gareth Evans was omitted from the match-day squad.
There was also no place in Kenny Jackett's set-up for Brett Pitman, despite him recovering from illness.
The away side had the first effort on goal in the fifth minute but Cameron McGeehan couldn't keep his shot down.
A minute later Ethan Hamilton exposed poor Blues defending when he was allowed to race into the box but his attempt on goal was well wide.
Sean Raggett should have done far better on nine minutes when Ronan Curtis flighted in a superb free-kick but the defender failed to get anything on it at the back post.
Trotters keeper Remi Matthews made the first real save of the game in the 25th minute when he pushed Curtis' 30-yard shot around the post.
The Irishman took the corner and James Bolton somehow turned over the bar from just four yards out.
The game had finally burst into life and Raggett was lucky not to be sent off on 27 minutes when he rashly brought down Joe Dodoo.
Luckily for the on-loan Norwich defender, referee Tom Nield drew a yellow card from his pocket rather than red.
From the subsequent free-kick, Hamilton crashed into the wall.
With 11 minutes remaining of the first period, the ball dropped kindly for Curtis on the edge of the box but he took a touch too many which allowed Tote Nsiala to make a block.
Steve Seddon's dead-ball deliveries were proving tantalising – and that’s how Pompey’s breakthrough was conjured on 42 minutes.
The left-back's free-kick cross the right was met by Raggett, whose header was kept out by Matthews.
The loose ball fell kindly for Burgess, though, who prodded home from close range to spark wild celebrations among the travelling Fratton faithful.
Bolton started the second period by far the better half, with the Blues barely unable to get out of their own half.
In the 53rd minute Dennis Politic jinked himself space before cracking a shot from just outside the box that was initially dealt with by visiting keeper Alex Bass before Raggett headed out for a corner.
Jackett tried to shift the momentum of the game by making a double substitute in the 56th minute, with Andy Cannon and Ryan Williams replacing Harrison and Marcus Harness
But just moments after coming on Williams brought down Brandon Flemming the left, but Bass made an assured take from Darcy's free-kick.
There was an initial burst of life from Pompey when Cannon won back possession deep in enemy territory before Cameron McGeehan’s effort was blocked.
Then the Blues were given a serious let off on the hour mark. Ronan Darcy’s inviting cross pinpointed Chris O’Grady lurking at the back post.
With the goal at his mercy, the substitute somehow got his finish all wrong and couldn’t deliver the Trotter the leveller they were searching for.
Cannon pepped Pompey up but they were failing to create any real goalscoring opportunities.
On the other hand, that man Darcy was proving a handful and another of his centres picked out O’Grady in the area. This time he got plenty of purchase of his header but steered well wide.
With 14 minutes remaining Politic again tried his luck from long range but Bass was equal to the attempt.
A Bolton equaliser was looking more and more likely – yet Bass was impregnable in the Pompey goal.
Politic played a one-two with Dodoo before his daisy-cutter was heading for the far corner, only for the academy graduate – who signed a new three-and-a-half year deal on Thursday – to tip around the post.
Four minutes of added-time set up a nervy finish, although the Blues held on for three points.
While it wasn’t impressive nor comfortable, it was job done as Jackett's troops remain seventh in the table but continue their assault on promotion.
Bolton: Matthews, Emmanuel, Nisala, Edwards (O'Grady 46), Flemming, Lowe, Hamilton, Darcy (Hall 89), Murphy, Dodoo, Politic.
Subs not used: Alexander, Brockbank, Thomason, Senior, Graham
Pompey: Bass, Bolton, Burgess, Raggett, Seddon, Naylor, McGeehan, Harness (Williams 57), Marquis, Curtis, Harrison (Cannon 57).
Subs: MacGillivray, Whatmough, Haunstrup, Close, WIlliams, Cannon, Hawkins.