Embiid will be suspended one game if he receives another flagrant-1 foul and two games if he receives a flagrant-2 foul.
Bontemps added flagrant points don't trigger in-game ejections, meaning any discipline wouldn't be assessed until the following game or games.
Marc Gasol fell to the ground when his arm locked with Embiid's on a free throw, and the Sixers center appeared to make contact with his face.
Embiid addressed the call after the game with reporters: "It's annoying, stupid... it's just basketball, I didn't mean to do it."
In the 76ers' first-round series against the Brooklyn Nets, Embiid received two flagrant-1 fouls for plays involving Jarrett Allen. The first came in Game 1 when Embiid elbowed Brooklyn's center in the face and again in Game 4 when he slapped across Allen's arm on a play that led to a skirmish on the court.
Embiid's flagrant-foul situation will be under a more intense spotlight if the 76ers are able to advance past the second round.
The Sixers and Raptors series is tied 3-3 with Game 7 scheduled for Sunday at Scotiabank Arena.