Duncan scored 25 points, claimed 13 rebounds and got plenty of help -- with Manu Ginobili adding 19 points, Michael Finley 17 and Tony Parker 14. The Spurs hit nine of 16 from three-point range and bounced back from a 13-point loss at Dallas Wednesday night.
Houston was led by Luis Scola with 20 points while Yao had 14.
Yao pulled Houston within two on a jumper with 1:54 remaining, but he missed two shots down the stretch, one of them blocked by Duncan.
San Antonio has won all six of its home games this season and the Spurs have split their two meetings with the Rockets. Houston has won only four times in its last 29 trips to San Antonio.