"We had a good rhythm going early in the third quarter and then we just kind of went flat," said Bulls coach Vinny Del Negro, whose team shot 10-for-40 in the second half.
Andrea Bargnani had 16 points and Hedo Turkoglu had 11 as Toronto evened its record at 4-4. The Raptors won for the third time when playing at home against an opponent playing the second game of a back-to-back.
Turkoglu left late in the fourth because of a sore left hip and will be reevaluated Thursday.
Denied a win over the Denver Nuggets on Tuesday night after a lenghty review showed showed Brad Miller's late jumper didn't beat the buzzer, Chicago came out gunning in this one, scoring 35 points in the second to take a 60-53 lead at the half and looking ready to eclipse its season high of 93 points.
Rebounding played a big part in the strong start, with Chicago using a 10-rebound advantage to outscore Toronto 14-0 on second chance points through the first two quarters.
In his halftime talk, Raptors coach Jay Triano made sure his players knew the rebounding disadvantage was unacceptable.
"He just came in and said, 'We don't need to fix it after the game, we need to fix it right now on the fly,'" Bosh said. "You have to give credit to all the guys. They did a good job of providing energy and stepping up when we needed it."
Toronto began undoing the damage in the third, outrebounding Chicago 15-7. Rookie DeMar DeRozan had seven for the Raptors, who cut it to 78-77 heading into the fourth.
"DeMar in the third quarter really gave us a lift," Triano said. "He chased balls, rebounded and was aggressive. I thought he had one of his best games as a pro."
Toronto finished with a 47-46 edge in rebounding.
Joakim Noah fouled out with 12 points and 11 rebounds and rookie Taj Gibson scored a career-high 18 points for Chicago, which went 6:14 without scoring in the fourth and lost its second straight following a three-game winning streak.
"We had good looks, we've got to knock them down," Deng said. "I don't know whether it's fatigue from the day before or what. We got a lot of looks that we didn't make."
Trailing 88-85 with 6:24 to play, Toronto surged ahead as the Bulls suddenly went cold. Bosh made a pair of free throws, Calderon's driving layup gave the Raptors their first lead of the second half, Bargnani made two free throws after a clear path foul by Noah and Calderon capped the run with a jumper, making it 93-88 with 5:04 left.
The Raptors scored six more points before Chicago finally broke the drought when Kirk Hinrich hit a free throw with 10 seconds to go.
"It's real frustrating knowing that we had the game," Rose said. "We started off well, played defense. To have to lose by not making shots toward the end kind of hurt."
Down 25-18 late in the first, Hinrich scored five quick points to pull the Bulls to within two, 27-25, after one.
After scoring eight in the first, Gibson opened the second by tying it with a breakaway dunk off a Toronto turnover. Deng scored eight in the second, including a jumper with 23 seconds left, as the Bulls took a 60-53 edge into the break.
With Aaron Gray (left leg), Jerome James (right Achilles) and Tyrus Thomas (left arm) injured, the Bulls again played with just 10 men. ... Chicago's next plays Saturday, when it hosts the Philadelphia 76ers. After that, the Bulls aren't at home again until Dec. 2, forced onto the road for six games by a circus at the United Center.