Tim Duncan added 15 points and 11 rebounds, Tony Parker had 13 points, six rebounds and seven assists and DeJuan Blair had 10 points and 11 rebounds as the Spurs won for the ninth time in 11 games and 17th in 20.
San Antonio's 46-9 record is tops in the NBA and the best 55-game mark since the Avery Johnson-coached Dallas Mavericks had the same mark in 2006-07 en route to a franchise-best, 67-win season.
Brook Lopez had 11 points and 10 rebounds to lead the Nets, who never led in the final roughly 30 minutes.
Travis Outlaw also had 11 points and Devin Harris and Jordan Farmar added 10 apiece for the Nets, who were held to 35 percent shooting from the field.
The Spurs never trailed after Duncan returned to the court early in the second period with the Nets ahead 34-31. A basket by Quinton Ross pushed the New Jersey lead to 36-31 with 9:08 to play in the half.
After that Duncan, Parker and Ginobili took over, helping San Antonio close the half with a 28-12 spurt that gave it a 59-48 lead.
Duncan hit two baskets inside early in the run, with the second on a pick and roll with Parker putting the Spurs ahead for good at 37-36.
Parker had six points in the quarter, the last three coming on a back-breaking three-point play after he drove through the Nets' defense seconds after Sasha Vujacic hit a 3-pointer with 5.9 seconds left in the quarter. George Hill also had six points points in the spurt.
New Jersey made a run late in the third quarter, drawing within 72-66 on a rebound follow by Lopez with 1:47 to to play.
Former Net Richard Jefferson then set up 3-pointers by Gary Neal and Hill around two free throws by Ginobili for an 80-66 lead after three quarters.
Ginobili scored the first eight points of the final quarter for the Spurs, hitting two long 3-pointers to help open a 88-68 lead that had the coaches clearing the benches.
NOTES: Nets rookie Derrick Favors picked up four fouls in eight minutes in the first half. ...The Spurs are 6-2 on their annual rodeo road trip with the final game scheduled in Chicago on Thursday. ...Outlaw showed what kind of night it was for the Nets, missing a wide open dunk attempt in the third quarter. ...San Antonio outrebounded New Jersey 50-39 and outscored them 40-28 in the paint.