The Mavericks also went scoreless for 5½ minutes during that stretch, their lone field goal coming as time expired.
Tony Parker had 21 points, and Manu Ginobili added 17. Kawhi Leonard had 11 points and 10 rebounds and Tiago Splitter pulled down 11 rebounds for top-seeded San Antonio, which has won 10 straight against Dallas.
Devin Harris scored 19 points for the Mavericks, who nearly pulled off a huge upset.
The Spurs had insisted that what happens in the regular season doesn't matter, and they were proven right for much of the game - much to the home fans' dismay. Absent were the crisp passing, aggressive defense and 3-point shooting that made for the league's best record.
San Antonio returned to its winning formula over the final seven minutes, taking an 86-81 lead with a 15-0 run. Splitter tied the game with about five minutes remaining, rolling to the basket off a screen for an easy layup off a pass from Parker.
The All-Star point guard then drove the lane for a layup and drained a 13-foot jumper, which he punctuated with a loud scream after Dallas called timeout with 2:45 to go.
Duncan, wearing a heavy brace on his left knee, walked off the court gingerly with 3:24 remaining in the third quarter after banging knees with Ellis. He did not get up as he customarily does during a timeout to greet his teammates.
Duncan later left the court, followed closely by trainer Will Sevening and team doctor Dr. David Schmidt, returning a minute later limping slightly less, and he played big down the stretch.
NOTES: Referee Joey Crawford screamed twice at a pair of scoring officials during a timeout, telling them at one point to do their jobs. Crawford, who once ejected Duncan for laughing from the bench during a game against the Mavericks, was booed regularly by the fans.
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