The Clippers have lost nine straight. They led by nine in the second quarter and by a point at halftime, but Los Angeles was outscored 31-15 by the Spurs in the fourth quarter and 63-40 in the second half.
"The defense got better as the game went on, and that fueled the offense," said Spurs coach Gregg Popovich, whose team scored 16 points in the first quarter.
The Spurs (24-11), winners of three consecutive games, have a 1½-game lead over second-place New Orleans in the Southwest Division.
Roger Mason added 18 points for the Spurs. Michael Finley had 15 and Manu Ginobili 13 off the bench. Matt Bonner scored 11.
Though Duncan fell short of double figures in points and rebounds (four), he led the Spurs with nine assists in 32 minutes.
The Clippers (8-27) got 21 points each from Eric Gordon and Al Thornton. Mardy Collins added 16.
San Antonio led by as many as 24 in the fourth quarter.
"In the second half, they hit everything they shot," Gordon said. "We have to change the way we play our game, like playing better on defense."
The injury-ridden Clippers are without Baron Davis, Chris Kaman and Zach Randolph. The lack of manpower showed in the second half.
"Playing short-handed means you have to leave some guys out there for some long minutes, and I did that with quite a few guys," Clippers coach Mike Dunleavy said. "I pulled the plug with about five minutes left."
Collins played 43 minutes, Thornton 42 and Gordon almost 40.
The Spurs broke open a close game by scoring the first 10 points of the second half. The surge was led by 3-pointers from Bonner and Finley, and it erased Los Angeles' one-point halftime lead and made it a 53-44 advantage for the Spurs after three minutes of the third quarter.
Finley went 4-of-6, including 3-of-3 from 3-point territory, for 11 points in the quarter. Bonner was 4-of-4 for nine points as the Spurs led by as many as 12 in the third.
"We started hitting shots," Mason said. "But the thing we wanted to continue to do was play defense, and I think our defense got better as the game went on."
The Clippers trailed 75-69 after the third despite shooting 53 percent from the floor. But they dipped to 4-of-20 shooting in the fourth quarter.
The Spurs have won the first two meetings between the teams this season.
The Clippers expanded an early two-point lead to six when the Spurs missed their final eight shots of the first quarter. San Antonio went 6-of-23 from the floor (26 percent) in the first quarter while Los Angeles shot 50 percent.
Most of San Antonio's shooting woes were from long range. The Spurs, No. 1 in 3-point shooting in the NBA, were 2-of-9 from the 3-point line in the first quarter and 5-of-17 at halftime.
They finished the game 11-of-29, hitting 6-of-12 in the second half.
Los Angeles led 22-16 heading into the second quarter when Collins found the basket from 14 feet. Collins scored eight first-quarter points after making 4-of-6.
The Clippers went up by nine on Brian Skinner's follow of Gordon's miss four minutes into the second quarter. It was their largest lead of the game.
But the Spurs cut the lead to 42-41 on a 15-footer by Parker with 1:25 left in the second quarter before the Clippers ended the first half with a 44-43 lead. Parker had 13 points in the first half, but so did Thornton. He led the Clippers with 6-of-8 shooting to go along with Collins' 5-of-7 showing from the floor.
Notes: Fred Jones, waived three days ago by the Clippers and reacquired by Los Angeles on a 10-day contract Thursday, was the first player off the bench for Los Angeles. He ended the game with 11 points in 33 minutes. ... Veteran Spurs G Jacque Vaughn was on the active list after spending the last three games in street clothes. He checked into the game with five minutes left, marking the first time he's played since Dec. 22. ... The Clippers have lost all 11 trips to the AT&T Center since it opened in 2002.
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