Terrence Ross scored 16 for the Raptors and Amir Johnson had 12 points and eight rebounds before leaving with a sprained right ankle. Toronto improved to 12-3 in its past 15 home games and moved six games above .500 for the first time since Feb 24, 2010, when it also was 31-25.
Johnson left at 5:41 of the third after rolling his ankle in a collision with Victor Oladipo. Johnson missed games on Feb. 10 and Feb. 12 with a sore right ankle, then came off the bench in Toronto's first two games following the All-Star break.
Raptors coach Dwane Casey said Johnson's injury didn't appear as serious as the one that sidelined him earlier this month.
"He got kicked in that spot, he didn't turn it," Casey said. "We'll see how he feels."
Toronto's next game is at Cleveland on Tuesday.
Harris had 10 points in the first quarter, but didn't score in the final 5:50 as Toronto closed the quarter on an 11-2 run to lead 19-14 after one.
Greivis Vasquez scored eight points in the second quarter and Johnson had six as the Raptors led 44-41 at halftime, but Casey wasn't too pleased.
"I think I've said this multiple times: we set basketball back 15 years in the first half," Casey said.
That changed after the intermission, when the Raptors took control by making 12 of 14 field goal attempts in the third quarter. Lowry made all five of his shots to score 17 points as Toronto outscored Orlando 36-24 to take an 80-65 lead into the fourth.
"We started setting better screens," Casey said. "We were more assertive coming off pick-and-rolls, attacking."
NOTES: After Washington and Philadelphia, the Magic close out this four-game trip by visiting Miami on March 1. ... DeRozan had four assists, raising his season total to a career-high 205. ... The Raptors won despite turning the ball over 24 times to Orlando's nine. ... The Magic are 14-15 at home this season. ... Orlando has lost nine of its past 16 regular-season meetings with the Raptors. ... Toronto G Nando DeColo, acquired from San Antonio on Thursday, made his Raptors debut in the fourth quarter. ... Toronto Maple Leafs players Jonathan Bernier and Troy Bodie attended the game.