SMU's Shake Milton missed a floater at the buzzer.
Stewart had 22 points for the Trojans (26-9). Bennie Boatright and Chimezie Metu each added 14 for USC, which advances to play No. 3 seed Baylor in the second round of the East region on Sunday.
USC also rallied from a big deficit in the second half in its First Four win over Providence.
Semi Ojeleye had 24 points and 10 rebounds and Sterling Brown had 17 points for SMU (30-5), which had won 16 straight.
SMU was in the NCAA Tournament after being banned from postseason play a year ago for multiple violations, including academic fraud and unethical conduct.