Stefanovic drove to the basket and converted an off-balance drive, falling to the court in the process. Griffin stepped on Stefanovic's chest as he turned to go back up court.
Officials reviewed the play and hit Griffin with a flagrant foul 2 and automatic ejection.
"We don't condone that," Illinois coach Brad Underwood told reporters after the game. "It's not part of anything we're trying to do with our program."
Underwood said Griffin apologized to Stefanovic.
No. 21 Illinois pulled away in the second half for a 79-62 victory in West Lafayette, Indiana.