Goals from Neil Danns, Lee Chung-Yong and Liam Trotter put Bolton 3-0 up inside the opening half an hour.
Danns scored an eighth-minute opener, bundling the ball home from close range after Jermaine Beckford played the ball across the face of goal.
Lee added a second on 19 minutes after capitalising on a defensive error from Joe Mattock and Trotter made it 3-0 with a fine dipping shot.
Mattock then scored what proved to be a consolation goal seven minutes before half-time, finding the net with a superb 25-yard strike.
Sheffield Wednesday manager Stuart Gray blamed the defeat on his side’s defensive frailties.
He said: “It looks like we’re going to need four goals to win any game at the moment because we’re gifting goals with individual errors.
“Our quality on the ball should have been a lot better. If I was to evaluate the season, I’d say the first 18 games were very poor and from December onwards it was better.
“We’ve now got dragged back down to being very poor again, which is disappointing.
“They did well and counter-attacked against us. They’ve got pace in the team, but we gave the ball away far too cheaply and didn’t close them down enough.
“It’s evident that our squad isn’t perhaps as strong in depth. There are a lot of players out of contract in the summer and I’ve evaluated what I’ve got.
“I know where I want to go with the club. It’s just a case of sitting down with the chairman and seeing what the budget is so that we know what players we can attract to the club.”
Bolton boss Dougie Freedman said: “It was very convincing. I felt that we had to make sure the first 20 minutes were done properly in terms of game plan and attitude because we were aware that Sheffield Wednesday would try to spring themselves into action.
“I felt that we were right on our game and deservedly went three goals up. We passed the ball very well from the back and through midfield.
“The hunger and desire was there as well. If anything, we probably should have scored more goals in the second half.
“Apart from a 10-15 minute spell Sheffield Wednesday had, I think it was a very convincing display.
“We will obviously bring one or two players in of the right profile over the summer and naturally one or two will move on. I’ve got to make sure that I’ve got one eye on the balance sheet.”