It was Toronto's second straight game without leading scorer Chris Bosh, and third straight loss.
"Obviously they were missing a great player, and it looked like we were going to be missing one, too," Magic coach Stan Van Gundy said. "He was sitting down so much with foul trouble."
Howard had only three points on 1-for-3 shooting until the fourth quarter, sitting most of the third after collecting his fourth foul. He seemed energized after the rest, and scored six straight in a 1:10 stretch that expanded Orlando's lead to 89-79 with six minutes remaining.
"He was most definitely frustrated," Lewis said. "But he came in the fourth quarter with fresh legs and finished it off for us."
T.J. Ford single-handedly kept Toronto alive in the fourth quarter. He scored 13 of his 20 points in the period, the first 13 the Raptors had. Anthony Parker added 19 points and nine rebounds and Jose Calderon scored 14 points, but Toronto lost its third straight.
"It's a big adjustment for us all, playing without Chris, because the guys have different roles," Toronto coach Sam Mitchell said.
Bosh scored 40 in the teams' last meeting.
Orlando is third in the Eastern Conference at 39-23, while the Raptors are fifth at 32-27.
Both teams were awful from the field in the first half -- particularly the first quarter. Orlando was 8-for-22 in the period, including just 1-of-11 on 3-pointers, while the Raptors shot 9-for-26. The Magic ended up 53 percent (40-of-76) compared with 41 percent for Toronto (36-of-88).
Howard, the NBA's dunk leader, had four in the final quarter, including two alley-oops.
"I didn't want to end up with a one-point night tonight. I was very upset -- not at my team, just myself," Howard said. "I got a little frustrated in the first half, and in the second half I played as hard as I could."
Keyon Dooling missed his second straight game with a sore left foot. ... The Raptors enjoyed an audible fan section. Orlando is a popular destination for Canadian tourists. ... Toronto concludes a three-game road trip Wednesday at Miami. Orlando plays Wednesday at Washington.