Lowry, who also had eight rebounds, notched his 20th straight game with at least six assists for the Raptors, who were coming off a 95-83 victory over the Knicks Friday at Madison Square Garden.
Terrence Ross drained seven 3-pointers en route to 23 points and DeMar DeRozan added 20 as Toronto picked up a sixth win in eight games overall.
Amar'e Stoudemire came off the bench to score 23 points and grab nine rebounds for the Knicks, who were without injured Carmelo Anthony for a third straight game.
Tyson Chandler put in 16 points as New York fell for the fourth time in five contests.
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