Terrence Jones provided 21 points and nine rebounds for the Rockets, who were playing without their leading scorer due to a thumb injury.
Jeremy Lin contributed 18 points and eight assists as Houston claimed the season series against the Spurs for the first time since 1996-97.
Boris Diaw netted 22 points and grabbed 11 rebounds for San Antonio, which was dealt a second straight loss for the first time this season.
Tim Duncan finished with 12 points and 14 rebounds.
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