After winning 15 games in a row, Denver has dropped two straight -- missing out on a chance at victory when Andre Miller's driving layup failed to go at the buzzer.
Ginobili's 3-pointer gave San Antonio a 100-95 lead, after which Denver's Danilo Gallinari twice went 2-of-2 at the foul line.
The last of those free throws brought the Nuggets within one with 34 seconds to go and the Spurs' Tim Duncan then missed a jumper with 12 seconds left.
That misfire did not wind up hurting San Antonio, however, when Miller failed to connect on his attempt at a game-winner.
JaVale McGee delivered 21 points for Denver.
The Spurs improved to 31-4 at home.