The Croatia striker fired home his first goal for the club after coming off the bench against injury-hit Everton.
David Moyes' side looked to have earned a point after fighting back from 2-0 down.
But Klasnic popped up late on to earn his side three points on Gary Megson's second anniversary in charge at Wanderers.
Tamir Cohen nearly gave Bolton a dream start when he headed just wide inside the first two minutes.
Kevin Davies then went close with a header of his own before Chung-Yong Lee fired the hosts into the lead on 16 minutes.
Sam Ricketts did well to get a cross over and the South Korean finished with aplomb.
Jo nearly snatched a fortunate equaliser on 24 minutes when his cross clipped the top of the crossbar but, instead, it was Bolton who doubled their advantage three minutes later.
Everton had looked unsteady under the high ball and when Matt Taylor lofted a free-kick into the area, Gary Cahill rose above Sylvain Distin to plant a superb header past Tim Howard.
But the Merseysiders were back in it on 32 minutes when the Wanderers defenders backed off Louis Saha and the Frenchman made them pay when he smashed a 25-yard rocket into the top corner.
Megson's men were guilty of sitting back and inviting Everton forward and on 56 minutes, Marouane Fellaini rifled home from a tight angle after running on to Tony Hibbert's ball forward.
Dan Gosling wasted a great chance to put Everton ahead when he raced through on goal but the youngster dithered instead of shooting and Fabrice Muamba was able to get back and make a vital interception.
And that proved costly as Klasnic pounced after Zat Knight's free-kick had dropped to him inside the area with four minutes left.