Danny Green scored 15 points, Tiago Splitter added 12 and Kawhi Leonard provided a double-double of 10 points and 11 boards for the Spurs.
Duncan, who had just returned to the lineup following a four-game absence with a sore left knee, limped off the court in the second quarter after sustaining a sprained right ankle and a sprained left knee.
The likely future Hall of Famer was injured while battling with Washington's Martell Webster for a rebound.
The Wizards got 21 points and nine assists from John Wall but still dropped their fourth straight contest.
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