Pompey old boy Matty Taylor and Ricardo Gardner handed Gary Megson's side a dream start.
And despite Peter Crouch's 12th goal of the season on 20 minutes, Wanderers went on to claim three deserved points in a one-sided contest.
Taylor, who joined Bolton for £3.5million in January, handed his new club the perfect start after just 52 seconds with a brilliant finish after flicking the ball over Hermann Hreidarsson's head before firing past David James.
It got even better for the home side moments later when Gardner ran on to Taylor's header across the face of goal from Jlloyd Samuel's long ball to smash home number two.
The Jamaican nearly grabbed his second when he volleyed wide from Gretar Steinsson's cross.
But Portsmouth were back in the contest on 20 minutes with their first attack of the match.
Niko Kranjcar picked out Crouch at the back post with a delightful cross with the outside of his right foot and the England forward headed home his fourth goal in as many games.
Johan Elmander should have restored Bolton's two-goal advantage but the Swede blazed over after a neat exchange of passes with Taylor.
Jussi Jaaskelainen then denied Kranjcar with a fine one-handed stop before Wanderers wasted another superb opportunity to kill off the visitors on 35 minutes.
First James saved Gardner's weak shot after the winger raced through on goal before Hreidarrson cleared Taylor's follow-up effort off the line.
Pompey were indebted to their goalkeeper again when, in first-half injury time, he somehow manages to turn Steinsson's point-blank header onto the post and Gary Cahill could not convert the rebound.
Portsmouth were fortunate not to fall further behind 11 minutes after the restart when James sliced his clearance but, with Elmander poised to pounce, the keeper saved his own blushes with a last-ditch tackle.
Kevin Davies' header from Gavin McCann's corner was then cleared off the line by Kranjcar, before Real Madrid-bound Lassana Diarra, who is set to join the Spanish giants in January for around £20miilion, was brought on.
But the midfielder could make little impact as Bolton continue to dominate with Kevin Nolan, Davies, Gardner, Elmander and Taylor all going close to extending the home side's lead as visiting manager Tony Adams' problems continue to mount.