The Rockets topped the Spurs, 97-90, rallying back from an early 15-point deficit in a battle of injury-depleted teams on Tuesday night.
Houston was missing James Harden, who was sitting out with a bruised thumb. San Antonio remained without Tiago Splitter, Kawhi Leonard and Danny Green, and during the third quarter, Manu Ginobili injured his hamstring after a dunk and never returned to the game.
Dwight Howard posted 23 points and 16 rebounds for the Rockets, shooting 13-of-25 from the free-throw line. Terrence Jones added 21 and nine.
Boris Diaw led the Spurs with 22 points and 11 boards and Tim Duncan contributed a double-double of his own with 12 and 14.
Houston absolutely dominated the glass, outrebounding San Antonio 55-39. Howard and company grabbed 19 offensive rebounds including several crucial ones down the stretch.
The Rockets shot only 26-of-47 from the charity stripe, but they were superb defensively to compensate for their ineptness at the line, holding the Spurs to 6-of-23 shooting from beyond the arc and a 43 percent clip overall.
San Antonio got off to a quick 21-6 start, and it looked like Gregg Popovich's group was about to run away with it. However, Houston gained some composure and whittled away little by little, trimming the lead to seven by halftime and eventually taking its first lead in the third quarter.
This marks the first time all season that the Spurs have lost back-to-back contests, and the Rockets have now won the first three meetings between the two ballclubs this year. That means Houston has clinched the season series against San Antonio for the first time since the 1996-97 campaign.