The Spurs closed the game by outscoring the Sixers, 15-3.
"When it comes down to the crucial time with three minutes left and up like that, those are the times we have to execute and be like the Spurs," said Jrue Holiday who had 15 points but shot 7 for 20 and committed six turnovers.
The Sixers still have not won consecutive games since they went 3-0 from Nov. 25-30.
"It would have been a hell of a win for our team against a very good team, and I thought we did a lot of good things," Sixers coach Doug Collins said. "But at the end of the day, our turnovers and our inability to execute when it counted was the difference in the game."
With the Sixers trailing by 84-83, Evan Turner missed a wide-open three-pointer from the corner with 1 minute, 18 seconds left.
Tony Parker increased the San Antonio lead to 86-83 on an off-balance jumper with 1:03 remaining.
Parker hit two free throws with 20.2 seconds left for additional breathing room as the Spurs improved to 33-11.
The Sixers, who visit Milwaukee on Tuesday, are 17-24 at the midway point of a disappointing season.
Turner had 18 points and 12 rebounds for the Sixers, while Spencer Hawes added 16 points.
Parker aided Duncan's effort with 20 points.
The Spurs did not panic when they got down. Duncan, known as the Big Fundamental, provides a quiet confidence, not to mention dominance inside.
"They made a run and we didn't make shots when we had to, so it is what it is," Duncan said. "We were lucky to get a win on the road."
Needless to say, this isn't where the Sixers wanted to be at the midway point of the season.
"We are very concerned, seven games under .500, and we are going to have to play over-.500 basketball to make the playoffs, so sure I'm concerned," Collins said. "That is why the game tonight is such a big game."
And then Collins stated the obvious.
"We have to find a way to put wins together and we can't be winning one, losing two," he said.
Collins insists there will be no panic with the team.
There is half a season to turn the corner and plenty of ground to make up.
Contact Marc Narducci at firstname.lastname@example.org or @sjnard on Twitter.