Bowen, averaging 8.3 points, finished with 17 points on 6-for-8 shooting, while Anthony, who came in with a 21.7-point average, scored eight on 4-for-15 shooting.
"My role is to play defense," said Bowen, who outscored Kobe Bryant 24-17 in a win over the Los Angeles Lakers during the week. "The way we play, with the constant ball movement, I get the benefit of a lot of open shots."
Anthony, who scored at least 20 in each of Denver's previous three games, blamed his performance on the lingering effects of a sprained left ankle that forced him to sit out five games.
"I could have been more aggressive in this one, but I'm scared to make a hard move on this ankle," he said. "This injury cuts in half what I truly can do."
Anthony sat out most of the third quarter after picking up his fourth foul. The Nuggets then rallied from a 10-point halftime deficit to pull within a basket late in the third.
Earl Boykins scored six straight points for the Nuggets, and
Marcus Camby made a pair of free throws in the final minute of the period to cut San Antonio's lead to 70-68.
"The effort we got today beats most teams," said Michael Cooper, Denver's interim coach. "We just have to find a way to win. ... We have to start thinking like champions."
San Antonio coach Gregg Popovich wasn't happy with the Spurs' lapses that allowed the Nuggets to keep close.
"We didn't have five guys focused and five guys executing at the same time," he said. "We have to sharpen up."
The loss was Denver's ninth in the past 10 games, and the team is 1-3 under Cooper. The Spurs have won 12 of their last 14.
A putback dunk by Duncan started a 12-6 run by the Spurs in the fourth that returned their lead to double digits. Bowen's final 3-pointer gave San Antonio its biggest lead at 95-82 with 2:42 remaining.
Kenyon Martin scored a season-high 26 points for the Nuggets, and Andre Miller had 16. Camby, back after missing two games with a back strain, had 10 points and 15 rebounds.
The Nuggets trailed by one when Parker made a short runner that started a 16-6 run to give San Antonio a 22-11 lead late in the first quarter. The Spurs made seven straight shots during the burst, three each by Parker and Duncan.
But the Spurs missed six of their first eight attempts in the second, and Denver pulled within 32-28 on a layup by Miller with 6:44 left.
After San Antonio called timeout, Ginobili hit a 3-pointer and, when Nene fouled him behind the arc, he made all three free throws. He finished with 11 points in the period, and the Spurs built their lead to as many as 12 points before the break.
Anthony went 2-for-7 for four points in the half.
San Antonio has the NBA's best home record at 17-1. ... Nuggets guard Greg Buckner missed his fourth straight game with a groin strain. ... Saturday's game, aired on ABC, was Denver's first on a national network broadcast since March 17, 1996. The Nuggets lost that game 91-81 at Detroit.