The Spurs led by one point heading into the final period, but they dominated the quarter while bouncing back from their first loss of the season.
San Antonio improved to 5-1 for the best early season record in the Western Conference.
Duncan went 9-of-12 from the field as part of San Antonio's overall 48-percent shooting effort. Patty Mills added 18 points off the bench while hitting 8-of-9.
San Antonio has split the first two outings of its four-game western trip that will continue with contests against Portland and the Los Angeles Lakers.