Kevin Nolan's first-half volley earned Bolton a first away league win since December 2005 as Portsmouth missed out on top spot in the Premiership.
Nolan brilliantly fired home from just outside the Pompey box after Linvoy Primus' headed clearance fell to him.
Pompey should have already been ahead, with Sol Campbell heading wide and Sean Davis side-footing against the post.
Benjani Mwaruwari twice shot wide from great openings either side of the break as Bolton held on to move up to sixth.
As well as denying Portsmouth the chance to go above Chelsea, they also succeeded in ruining Milan Mandaric's big night as the ex-chairman said goodbye after seven years at Fratton Park.
He nearly saw his team get off to the perfect start, as twice in the first five minutes they went agonisingly close to an opener.
Campbell missed the first chance, glancing a header wide of the far post having met Matt Taylor's inswinging corner unmarked six yards out.
Moments later a lovely cushion header from Benjani teed up Davis 16 yards out, but his controlled right-foot shot cannoned back off the post into Jussi Jaaskelainen's grateful arms.
Pompey were dominant, with Jaaskelainen parrying a Kanu shot away and then brilliantly diving to his left to tip behind a goalbound Taylor volley from just inside the penalty area.
It was classic Bolton to take the lead with their first attempt on goal.
A free-kick into the Pompey box was headed out by Primus into the path of Nolan, who executed a perfect volley to arrow the ball into the corner from 22 yards.
It was the first Premiership goal the hosts had conceded this season and it subdued the crowd after a vociferous opening.
They were out of their seats when Benjani raced through before the break, but he could only lift his shot over Jaaskelainen and wide after hesitation from Abdoulaye Faye.
The Zimbabwean had another gilt-edged chance to level when he shrugged off Abdoulaye Meite, only to slice woefully wide in front of goal.
The longer the game went on, the more it suited Sam Allardyce's men, who sat back and invited Portsmouth onto them, breaking whenever they got the chance.
Nolan should have doubled the lead when a long throw fell to him six yards out, but the midfielder uncharacteristically blazed over.
Pompey were struggling to break down Bolton's rock-solid defence and instead took to shooting outside the area, with Glen Johnson rifling fractionally wide from 25 yards.
A flurry of late corners created some pressure and Nolan in particular made several brave blocks as Bolton held on for a gutsy three points.
Bolton 1 - 0 Portsmouth
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