The Spurs were already without LaMarcus Aldridge, who was ruled out for the season after having right-shoulder surgery in April.
"We're down a little bit, but for us, in our specific situation, development is more important than anything right now," head coach Gregg Popovich said. "I'm not too concerned with trying to figure out how to match up with the Lakers or Clippers or Celtics or Raptors or Rockets or Nuggets or anybody else."
Lyles was averaging 6.4 points and 5.7 rebounds in 63 games for San Antonio this season.
The 6-foot-9 Lyles is in his first season with the Spurs. The 53 games he started this year are the most in his five NBA seasons.