The Bulls, coming off a controversial setback against Denver Tuesday, owned an 88-85 lead after Taj Gibson made two free throws with 6:13 to play. Chicago did not score again until Kirk Hinrich made a free throw with 5 seconds left.
In between, Calderon, Chris Bosh and Andrea Bargnani teamed to score all of the points in the game-closing surge.
The Bulls fell for the second night in a row, having had an apparent victory over Denver taken away Tuesday after game officials viewed video replays. A shot by Brad Miller appeared to be good as the final buzzer sounded but officials determined the shot was taken after the final second had ticked off the clock.
Bosh led Toronto with 28 points Wednesday, helping the Raptors end a two-game losing streak. Calderon had 18.
Chicago was paced by 18 points from Gibson and Luol Deng.