Cam Thomas had 24 end Cam Johnson 17 as Brooklyn fell to San Antonio.
The Spurs shot 54.7 percent from the field and 46.2 percent from 3-point range.
Without Webmanyama, San Antonio scored 62 points in the paint and were led by Devin Vassell's 37.
Brooklyn dropped its fifth in a row and will look to get right on Thursday back home at Barclay Center against the Golden State Warriors.