The 23-year-old, who has undergone three knee surgeries in as many years and missed the first 24 games of the season, hyper-extended his right knee in the second quarter and sat on the court for a few minutes before limping to the locker room.
Bynum will undergo an MRI scan on Wednesday but the team sounded confident he would be on the court for the play-offs.
Bynum had been a key component in the Lakers' 17-1 stretch before the recent losing stint.
"I went in at halftime to talk to him and he said: 'I'm going to be alright,'" Los Angeles coach Phil Jackson said during the game. "I think he has a good idea about it because he's been through this before."
With the game tied 83-83 midway through the fourth, Los Angeles went on a 19-5 run to finally put away San Antonio, who had long clinched the top seed in the conference.
The Lakers, the defending NBA champions, can secure the second seed with a season-finale win against the Sacramento Kings on Wednesday.
Lamar Odom, who will be starting in Bynum's place against the Kings, finished with 23 points. Pau Gasol added 17 points and 17 rebounds but the Lakers are still searching for the form that took them to two consecutive NBA titles.
"The play-offs (are coming) at a perfect time for us," Odom said. "We need a little break to recuperate, watch tape and get better."