Willie Green led Philadelphia with 21 points and Andre Iguodala scored 19. Samuel Dalembert added 12 points and 20 rebounds for the skidding 76ers, who have lost seven straight.
Ginobili hit four 3-pointers, his only field goals of the entire game, in the last quarter to help the Spurs pull away.
Heading into the final 12 minutes the 76ers were up 65-64 after San Antonio's miserable third quarter allowed them to take the lead.
Philadelphia went up by as many as five early in the fourth, but the Spurs crept up to tie the game three times before Ginobili helped them pull away. The Spurs' super-sub had gone 0-of-6 from the field before his back-to-back 3s gave the Spurs an 81-77 lead with 3:41 to play.
Ginobili hit another pair of consecutive 3s to give San Antonio an 89-78 lead with 1:46 on the clock and effectively put the game away.
The Spurs took the lead until midway through the third quarter with 1:33 to go in the first when Francisco Elson broke a 24-all tie by tipping in Ginobili's 3-point miss with his back to the basket.
And while the Spurs again struggled early, as they have in recent games, they managed to take a 27-24 lead into the second quarter.
An 11-1 run that began with Duncan's surprisingly easy dunk over Dalembert gave San Antonio a 47-35 advantage with 4:38 to go in the second quarter. The Spurs were up 52-46 at halftime.
The Spurs fell apart during the third. They hit just 3-of-22 (14 percent) from the field and scored 12 points, a season-low for scoring in the third quarter. They missed 16 straight shots in the last 8:33 of the quarter.
Philadelphia wasn't exactly on a scoring rampage, either, hitting just 4-of-16 from the field (25 percent). But the 76ers did enough to take a 59-58 lead with 7:32 to go off a free throw from Iguodala, who scored eight points in the quarter.
The 76ers took the lead again, 61-60, with 6:23 to go off Iguodala's jumper.
Notes: Spurs coach Gregg Popovich said injured G Brent Barry (torn muscle in left calf) is probable for Thursday's home game vs. Cleveland. ... The Spurs celebrated the franchise's 35th anniversary with a halftime tribute Monday.
