The Raptors clinched a playoff spot with a loss by Chicago despite the defeat to the Celtics.
Lowry suffered the injury in Toronto's win over Orlando on Sunday. He played 40 minutes in that game, scoring 18 points.
Raptors coach Dwane Casey said before the game that he won't hesitate to rest players down the stretch to keep them fresh for the playoffs, even though Toronto is right behind Cleveland for the No. 1 seed in the East.