The All-Stars and Olympic teammates became tangled in the third quarter of Houston's 105-103 victory over Cleveland on Sunday. Harden fell back to the court, then kicked his foot up into James.
Corey Brewer is making his first start in place of Harden, who is missing his first game this season.
Brewer has averaged 12 points in 33 games with Houston and 11.3 in 57 games overall.
Harden is averaging 27.1 points this season.
The Rockets are 41-18 following a five-game winning streak. Atlanta leads the NBA at 47-12.
Harden is expected to return for Wednesday's home game against Memphis.