The goal came in the second half after Tigers new-boys Jozy Altidore and Kamel Ghilas combined to fire the home side to their first three points of the campaign.
Bolton were gifted a tremendous chance early on as the Hull defence failed to pick up on a throughball from Fabrice Muamba, allowing Johan Elmander time and space inside the Hull box.
But the Sweden striker failed to hit the target as he dragged his right-footed shot wide of the post from close range.
Geovanni came close on the half-hour mark as the Brazilian let fly with a shot from 25 yards, but keeper Jussi Jaaskelainen neatly turned the ball away for a corner.
Matt Taylor then came close for the visitors as his low free-kick from 20 yards was well saved by keeper Boaz Myhill, who only saw the ball at the last moment.
Kevin Davies had a great chance on the stroke of half-time as Sean Davis delivered a pinpoint free-kick onto the right foot of the striker, but his side-footed volley from close range saw the ball float wide of the mark.
Davies then came within inches of scoring for the visitors early in the second half as Taylor curled in a free-kick from the right onto the head of ex-Southampton man, but again he failed to get his effort on target as the ball bounced just wide of the post.
Hull opened the scoring on 61 minutes. Substitute Altidore made an immediate impact with a ball over the top of the Bolton defence into the path of Ghilas, who made no mistake from eight yards with a blistering strike into the bottom corner of the net.
Altidore then had the chance to score on his debut for the home-side as Geovanni found the American international in space with a clever ball, but the Villarreal loanee could only watch as his shot bounced agonisingly wide of the post.
Ghilas came close to grabbing his second on 75 minutes but the Algerian could only fire his left-footed shot against the Bolton crossbar.
Altidore had another chance moments later but his turn and shot inside the box was well saved by Jaaskelainen.
Myhill then made a tremendous double save in injury time to seal the win for Hull.
He first saved a low shot from ex-Hull man Sam Ricketts and then did enough to turn away the rebound from substitute Chung-Yong Lee to ensure a clean sheet.