Matt Bonner also sat out Saturday night's game with a strained right calf.
Despite playing short-handed, the Spurs still picked up their 13th straight win, 99-90.
Spurs coach Gregg Popovich has been known to rest his veterans at times during the regular season, especially when playing road games on consecutive nights. San Antonio won 99-79 at Sacramento on Friday night.
Duncan, Ginobili and Tony Parker all sat out San Antonio's 104-102 win against the Warriors on Dec. 19. Parker got the start Saturday night at point guard and had 20 points and five assists in the win.
Warriors swingman Andre Iguodala was inactive for the third straight game with tendinitis in his right knee.
The Associated Press contributed to this report.