The result was an eighth straight victory for the defending NBA champions, who inched closer to securing a playoff spot.
The Warriors, meanwhile, are still in a tight fight to reach the postseason.
"You know it's going to be a high-paced game," Duncan said. "You know they're going to want to get shots up quick. I thought transition 'D' was really good for us. We got back and got in front of them. If we take away a lot of the easy stuff, if usually works to our advantage."
The Spurs remained second in the Western Conference, just percentage points behind the New Orleans Hornets.
The Warriors, in a three-way race with Dallas and Denver for the final two playoff spots, dropped their 20th straight in San Antonio since the Spurs drafted Duncan in 1997.
"On offense Tony did another great job running the show for us and distributing and scoring," said Spurs coach Gregg Popovich. "Timmy was great in the hole. I thought everybody really contributed and knocked down shots and moved the ball well."
Baron Davis led the Warriors with 19 points in a game the Spurs controlled most of the way.
"The shots they were giving us we could not make. I thought they were good shots for us," Golden State coach Don Nelson said. "And we had two of our best players, both of them had their worst games of the year. We're going to have a hard time winning when that happens."
Golden State visits Dallas for a crucial game on Wednesday night. With Denver's win on Tuesday, the Warriors fell from eighth to ninth in the West.
"It's just like last year - it's just that we have a better record this year, but we're still fighting to get in the playoffs like last year," Jackson said. "This one was definitely tough, but we're a tough team. We've got another game tomorrow and we've got to be ready to play that one. We still have a chance to get in and our focus is getting in."
The Warriors shot 37.5 percent from the field to the Spurs' 55 percent and San Antonio had the advantage in rebounding (54-37) and assists (25-8). The Warriors had scored at least 100 points in 37 straight games before Tuesday's loss.
Parker, with his floating jumpers and acrobatic layups, and Duncan were almost solely responsible for a 20-8 run in the second quarter that took the Spurs from tied at 40 to a 60-48 lead with less than a minute to play in the half.
The Warriors got as close as 67-63 in the third when a wide-open Jackson hit a 3 from the top of the arc with 6:19 to go. It was only his second basket of the night.
Ellis got the Warriors within two before the Spurs went on an 11-0 run to close the quarter -- again highlighted by Parker's prowess, and back-to-back 3s from the corner from Bowen -- to put them up 86-73 with a quarter to play.
"It happened in a matter of two or three minutes. Their lead went from eight to 20," Davis said. "I thought we took a lot of jumpers, but at the same time we do that. They did a great job of playing good team ball and great team defense. They kept plucking and kept plucking."
San Antonio's role players got into the action early in the fourth. Ime Udoka followed a layup with a 3, and backup point guard Jacque Vaughn hit a 3 from the corner to give San Antonio its biggest lead of the game to that point, 94-73, with just under 10 minutes to play.
- The Spurs announced Tuesday that they signed F Bobby Jones of the NBA Development League's Sioux Falls Skyforce to a 10-day contract. Before being reacquired by Sioux Falls in late March, Jones had played in 42 NBA games this season for Denver, Memphis, Houston and Miami.
- Golden State won the season series 2-1.
- The Warriors might see Dirk Nowitzki on Wednesday after the Mavericks upgraded his status to day-to-day on Tuesday. Nowitzki sprained his left ankle and knee on March 23. "I'm glad to see him back, it may surprise you, but I'm very glad to see him back," Warriors coach Don Nelson said.
- The Warriors said C Andris Biedrins jammed his right big toe in Sunday's win over Dallas. Biedrins came off the bench in the first quarter with 3:19 to play.
- Popovich got a technical with 10:02 left in the first half. Golden State's Davis got one after getting tangled up on the floor with San Antonio's Oberto after a jump ball call late in the third.