Duncan finished the game with 19 points and 16 rebounds and Spurs coach Gregg Popovich notched the 700th regular-season win of his career.
Indiana went ahead 99-98 with 1:12 left on a tip-in by Roy Hibbert, who scored 20 for the game. After San Antonio missed two shots and Indiana one, Duncan got the ball in low but Hibbert blocked his shot. Duncan grabbed the rebound and jammed it home for the winning score.
Tony Parker had 15 points for San Antonio and Keith Bogans added 14.
Troy Murphy led Indiana with 21 and T.J. Ford scored 14.
The Pacers trailed 50-45 at halftime but led 83-70 at the end of three quarters.