Carlos Delfino scored 23 points and was 6-for-7 on 3-pointers, and T.J. Ford added 16 points and seven assists for the Raptors, who have won all three meetings with the Pacers this season.
Danny Granger and Marquis Daniels each had 20 points, and Granger added 10 rebounds for the Pacers.
Toronto led by eight at halftime, but Indiana trimmed its deficit to 58-55 on a layup by Mike Dunleavy.
Indiana led 86-84 before Toronto went on a 13-2 run that included two 3-pointers by Delfino to take a 97-88 lead with just over 4 minutes to play.
A dunk and a jumper by Daniels cut Toronto's lead to 101-98 with 40 seconds to play.
Ford missed a finger roll on the other end, and Granger rebounded, giving the Pacers a chance to force overtime. But Kareem Rush missed a 3 with 11 seconds left.