Ginobili had missed five games because of a sprained left index finger, and had his hand wrapped to protect the injury.
"I was feeling good all game long. I just didn't make the shots that I usually make, but I just stayed patient and let it come to me," said Ginobili, who went 5-of-12 from the field and 12-of-13 from the line.
The Spurs, who started the season 17-3, have gone 6-6 in their last 12 games and Duncan is happy to have Ginobili back.
"He's our finisher. He's our attacker and he just adds another dimension to our team, especially down the stretch," Duncan said. "When plays don't work or things aren't working exactly right, someone like that can break down a defense.
"He's a great guy to make things happen and find open shots for people. And we missed that the last few games."
Duncan hurt his left knee in a collision with Corey Maggette as the Clippers' forward fouled out with 1:27 left. Duncan missed both free throws before going to the bench, but doesn't expect to miss any playing time.
"It was incidental. We just went knee to knee and I think I got the worst of it," Duncan said. "It went numb for a while, but it feels a lot better now. It's going to swell a little bit, obviously, but hopefully by tomorrow it'll be fine."
The game was close most of the way, with the Spurs opening their biggest lead at 85-77 when Parker made one of two free throws with 3:10 remaining.
He had put San Antonio ahead to stay when he hit a 3-pointer from the left corner for a 76-74 lead with 5:21 to play. His wife, actress Eva Longoria, was sitting courtside along the baseline, some 5 feet away.
He said afterward that he was focusing only on the shot.
"I was just thinking about the play and being ready. They swung it to me and I was wide open," Parker said. "The play was designed for Timmy [Duncan] for a post-up, but they went to double-team him and it ended up in my hands."
Los Angeles made a game of it, playing mostly solid defense and getting 20 points and 14 rebounds from Chris Kaman, and 17 points and eight boards from rookie Al Thornton. Maggette had 14 points.
"Overall, we did a decent job," Kaman said. "We played better than we have in the past. We did well defensively. It was there, but the last three minutes, we just didn't finish, which has been a common problem for us.
"This is a step in the right direction."
Los Angeles coach Mike Dunleavy agreed.
"I thought our guys played well," he said. "We held them to 40 percent shooting. We had some good ball movement, but the difference in the game was the free throw line."
San Antonio had 36 free throws to 12 for Los Angeles, with the Spurs making 25 and the Clippers good on eight.
San Antonio's Michael Finley made only one of his 10 shots, but had 11 rebounds to help the Spurs beat the Clippers for the eighth time in a row and 15th in their last 16 meetings.
Ginobili's two free throws gave the Spurs a 64-62 lead heading into the fourth quarter after the teams swapped the lead back and fourth in the third.
Tim Thomas was back for the Clippers after being sidelined for four games by a sore left knee. He had seven points.
After San Antonio fell behind 37-27 with 7:35 left in the second quarter, Duncan had 10 points, six rebounds and two steals to lead a 15-5 run that sent the game into the break tied at 42.
San Antonio G Brent Barry missed his fifth game in a row with a torn left calf muscle. ... Los Angeles F Aaron Williams sat out his ninth game because of a sprained left wrist. ... The Spurs, who got off to a 17-3 start this season, are 6-6 in their last 12 games. ... Duncan had 34 points on 12-for-22 shooting, with 18 rebounds, in San Antonio's 99-90 victory over the Clippers on Dec. 22. ... The Spurs were 3-for-18 from 3-point range.