Chicago played without the injured Luol Deng (hip), Joakim Noah (foot) and Taj Gibson (knee). At least Richard Hamilton (back) returned from his 19-game absence, but he could not help the battered frontcourt.
The Bulls fell behind early as Toronto shot about 20 percent better from the field in the first 18 minutes.
The Raptors had their choice of open looks for much of the half and picked the Bulls apart. Five Raptors finished in double-digits and two more scored eight points.
Jimmy Butler's stellar start kept Chicago in the game. He finished with a game-high 28-points and Carlos Boozer scrapped out double-double.
Butler triggered an 8-0 run capped by Nate Robinson's triple with three minutes left in the second quarter. Suddenly, the Bulls trailed by just four points at the break, despite Toronto outshooting them by a wide margin (54.1 percent to 42.6 percent).
Chicago's 22-17 advantage on the boards helped compensate for their poor shooting, especially the 8-1 advantage on the offensive glass.
But the Bulls failed to bring the momentum they created at the end of the first half into the second. Toronto outscored them 27-18 in the third quarter and they trailed by 16 with only eight minutes remaining.
And just as in the first half, the Bulls went on another run to keep the game interesting. Robinson and Butler again joined forces as Chicago scored 10 unanswered points. After falling behind by nine in the final two minutes, Robinson and Boozer pulled the Bulls within just two points as 16.8 showed on the clock.
But it was too little, too late. Little Nate missed a free throw and couldn't get a desperation shot to go, as Chicago's rally came up short.
With the loss, the Bulls fall to 42-35 and their lead over the Atlanta Hawks shrinks to half a game. Still, sixth place doesn't seem so bad when you consider that it would avoid the Miami Heat in the second round.
But Chicago would have to get out of the first round for that to matter, and their postseason hopes look dim unless Deng and Noah can heal up significantly in the next 10 days.