Matt Taylor got the only goal on 50 minutes and then a sublime second-half goalkeeping performance from Jussi Jaaskelainen saw Gary Megson's side claim victory.
Hull nearly took the lead in style in the first half as Geovanni turned provider with a cross from the left towards Marlon King, who cleverly rose to flick the ball with the back of his heel onto the crossbar.
Daniel Cousin came close on the half-hour mark as George Boateng floated in a cross from the left onto the head of the striker, but he could only glance his header just wide from eight yards.
The visitors were gifted a chance towards the end of the half as a mix-up between Paul McShane and Boaz Myhill allowed Ricardo Gardner to nip in on the byline and play the ball across an open goal but no Bolton players were there to capitalise.
Bolton took the lead on 50 minutes as Hull failed to clear a Gavin McCann corner, allowing the ball to fall to Taylor inside the area, who struck a first-time left-footed shot passed the outstretched Myhill and into the back of net.
Midway through the half Hull were awarded a free-kick just outside the box after Fabrice Muamba was penalised for a foul on Dean Marney. Geovanni curled the ball with precision towards the top corner, but Jaaskelainen pulled off a great save to deny the Tigers.
Jaaskelainen was then on hand to make a tremendous double save as yet again he denied Geovanni.
The Finalnd international showed great reactions to stop an arrowed header from the Brazilian and then a Michael Tuner effort from the rebound.
Moments later Geovanni picked the ball up, ran and fired in a low shot but again Jaaskelanien was there to pull off a good save.
Unbelievably Jasskelainen then made another outstanding double save as first he palmed away a rasping deflected effort from King and then managed to dive to his right to flick the ball off Geovanni's toe to deny what looked a certain goal.
Ian Ashbee came close to equalising towards the end of the game, but his rifled shot from 20 yards flew just over the bar.