Portsmouth are still looking for their first away win of the season as Kevin Davies' 53rd minute winner gave Bolton a welcome home success.
Sam Allardyce's side had previously only won two Premiership games at the Reebok Stadium this season while picking up six draws and for long periods this game looked to be heading for a stalemate.
Davies put that right with his sixth goal of the season but Pompey had their moments, especially when a Yakubu Ayegbeni shot was deflected onto a post by Bolton defender Emerson Thome.
However, the home side should have added to their goal tally, both Davies and Youri Djorkaeff missing good chances, although Pompey's spirited finish had Bolton worried at times, especially when Patrik Berger went close while Teddy Sheringham wasted a golden chance when he hooked the ball high over the bar.
Wanderers gave Javier Javi Moreno his full debut against an unchanged Pompey side that was bidding to pick up their first back-to-back wins in the Premiership after beating Manchester City last week.
Moreno, who is at the Reebok on loan, was hoping to be Allardyce's answer to the club's lack of goals.
Yet it was in defence where Allardyce's concerns lay in this game, especially at left back, after Jamaican international Ricardo Gardner was ruled out until the end of the season with knee ligament damage.
Also missing was Simon Charlton, who pulled a hamstring in the win at Blackburn seven days earlier, but he did manage to make the subs bench.
Also on the bench was former AC Milan midfielder Ibrahim Ba, who extended his loan deal with the club until the end of the season.
Portsmouth again included Eyal Berkovic, manager Harry Redknapp's recent signing from Manchester City.
Wanderers however were the first to show their attacking teeth and it could have been a dream start for Moreno.
The Spaniard received the ball inside the area after good work by Djorkaeff, but despite making good contact he was unable to direct the ball on target.
There was some anxiety in the home defence when Berger picked up an Ivan Campo pass, but Thome was on hand to cut out the danger.
Both sides were guilty of being ponderous in attack, although Pompey were fortunate to escape two strong penalty claims from Wanderers. Djorkaeff looked to be held back by Arjan De Zeeuw before Linvoy Primus seemed to use his hand to clear a dangerous ball into the area.
Even so, Wanderers should have taken a 37th minute lead when Nicky Hunt worked his way to the byline, but with Moreno and Davies waiting to take the ball in the six-yard area, the young full-back wasted the opportunity when he over-hit the cross.
Within a minute of the restart, Shaka Hislop pulled off a good save to deny Jay-Jay Okocha whose shot was heading into the top corner.
However, almost immediately the keeper was left shaking his head after he gifted Bolton the lead.
Djorkaeff started the move, playing the ball into the area for Hunt, whose cross into the six-yard box was deflected towards goal by Davies, but although Hislop looked to have the goal covered, it rolled under his hand and into the net.
Bolton, however, had a scare of their own moments later when Yakubu's shot was deflected past Jussi Jaaskelainen by Thome, but the defender was relieved to see the ball hit a post and rebound clear.
Hunt then played in Djorkaeff with a clever ball to the far post, but this time Hislop was on hand to push the ball wide.
Hunt then set Davies up, but the full-back was disappointed to see his efforts wasted again when the striker put the ball over the bar.
Portsmouth responded with their best chance of the game, Alexei Smertin firing in a hard, low shot that Jaaskelainen had to go full length to push round the post.
Smertin then set up another good chance with a run to the byline but Sheringham headed his cross high over the bar.
Berger then went close with a shot that flew past the far post.
Pompey made it a nervous finish for Bolton, but two minutes into injury time their last chance went begging when Dejan Stefanovic was sent off for a foul and abusive language.
Man of the match: Nicky Hunt: Not only set up the match-winner for Davies but produced two other, gilt-edged chances that should have been converted into goals.