The Blazers had to regroup after blowing a 16-point lead in the fourth quarter to emerge with their first win in three games.
DeMar DeRozan poured in 14 of his game-high 36 points in the fourth quarter as the Raptors charged back from a 98-82 deficit, including two foul shots with 25.4 seconds left for Toronto's first lead.
But Lillard (21 points) banked in a floating shot from the lane to restore the Blazers' advantage.
DeRozan turned it over on the next possession and Nicolas Batum sealed the victory with free throws with 0.1 seconds left.
LaMarcus Aldridge paced Portland with 27 points with 15 rebounds.