Lowry drained four 3-pointers during the third-quarter surge, in which the Raptors outscored the Magic 36-24 to grab control of the contest. He finished with 28 points overall while DeMar DeRozan scored 24 and Terrence Ross added 16.
Amir Johnson put in 12 points for Toronto.
Tobias Harris netted 28 for Orlando, which lost a 15th straight on the road. E'Twaun Moore scored 16.