Deng made a put-back shot for the Bulls as time expired after James Johnson blocked C.J. Watson's shot. The play was reviewed by the officials to confirm Deng had released the ball prior to the buzzer.
"I saw the light after I shot it, but I still wasn't sure how close it was," Deng told reporters. "Toronto played great. And we just found a way to win."
With the score tied at 100-100, the Raptors (16-33) missed three of four foul shots in the final 15 seconds to give the Bulls their opportunity.
"We had every excuse in the world to lay down and give in to a good team like Chicago," said Raptors coach Dwane Casey, who was without guards DeMar DeRozan and Jerryd Bayless.
"But our guys played with heart and with toughness, and I promised them if we continue to play like that and we get some more guns in, that style of play will win the NBA."
The Raptors charged to a 30-20 first quarter lead and after squandering the advantage early in the second they got their noses back in front 55-50 at halftime.
The Raptors missed three consecutive shots for the win in the final 10 seconds of regulation, setting up overtime.
"They (Raptors) deserved it, They were playing a lot harder than we were," Bulls coach Tom Thibodeau said.
"I have a problem with the way we played. It's everybody. It starts with me. I have to do a better job of having them ready."
Carlos Boozer led the Bulls (40-10) with 24 points and 10 rebounds and Deng also registered a double-double with 23 points and 10 rebounds.
League MVP Derrick Rose missed his sixth consecutive game and the Bulls were without Joakim Noah in the second half after he was ejected for two technical fouls in the second quarter.
Johnson and Jose Calderon led the Raptors with 20 points each and Gary Forbes had a double-double with 12 points and 13 rebounds.