The winners raced out to a 35-24 lead after the first quarter and the margin grew to 66-49 at the half.
The closest Houston came in the final 24 minutes was 89-71 on Carl Landry's jumper with 8:38 left.
Manu Ginobli scored 14 points with five rebounds and three assists.
It was San Antonio's seventh win in a row, helping it maintain at least a share of first place atop the Southwest Division with New Orleans.
Houston was led by Luis Scola's 24 points and seven rebounds. Tracy McGrady scored 13 with six assists and three rebounds.