Neil Danns, Lee Chung-yong and Liam Trotter scored for Dougie Freedman's men before Joe Mattock scored what proved to be a consolation goal for the hosts before half-time.
Both sides are free from relegation, or the play-off fight, but Wednesday will head into the summer having failed to win their last four home league games.
Wednesday midfielder Giles Coke tried a shot from distance early on which was saved by Adam Bogdan.
Michail Antonio then tried a long-range effort which sailed over Bogdan's crossbar.
Bolton went close to scoring with their first effort of the match when Matt Mills' header was deflected over following Lee's corner.
Danns opened the scoring soon after, bundling the ball over the line from close range after Jermaine Beckford did well to get to the byline and put the ball across the face of goal.
After Antonio chested the ball down and smashed his shot off-target, Lee increased Bolton's lead when a defensive mistake allowed him to run through the middle and slip the ball under the advancing Chris Kirkland.
Rhys McCabe threatened to pull a goal back for the hosts when he fired in a firm low drive, but Bogdan got down to his left to save.
Trotter sent Bolton further ahead with a superb dipping effort from around 25 yards out which left Kirkland flapping.
After Jeremy Helan's header was easily saved, Mattock reduced the areas with a fine strike, hammering the ball beyond Bogdan following a corner.
As the half drew to a close, Danns and Caolan Lavery had efforts saved at either end.
Danns looked certain to restore Bolton's three-goal lead early after the re-start when he found himself through on goal, but Kirkland stretched out a hand to claw the ball away as the midfielder prepared to go past him.
Bolton continued to threaten with Lee shooting off-target and Robert Hall putting a free-kick over.
Wednesday rarely threatened to make a game of it. Helan's angled shot was easily saved by Bogdan and Atdhe Nuhiu dragged his low shot wide.
Kirkland prevented Danns from scoring his second goal of the match, saving with his legs after the midfielder received a pass from Lukas Jutkiewicz.
Lee should have added a fourth for Bolton when Andrew Kellett's ball picked him out inside the area, but from around eight yards out he fired wide of the target.