Shake Milton added 22 points for the Mustangs (7-2), who stretched their home winning streak to 28 in a row. Jimmy Whitt had 14 points and Jarrey Foster 13.
Chimezie Metu had 13 points to lead USC, which had won its last seven non-conference road games.
It was the third meeting in 13 months between the teams. The Trojans (4-2) won both games last year, including a home game in November 2016 and then again in the first round of the NCAA Tournament last March.
The Mustangs are 31-0 at home under coach Tim Jankovich, including three games when he filled in for Larry Brown when he was still an associate head coach.
SMU was down 37-33 before Emelogu hit a 3-pointer that ignited a 23-5 run. The Mustangs went ahead to stay after Milton's two free throws with 15:31 left made it 38-37. Emelogu had three 3s and a dunk in the stretch.
After Metu's dunk with just over 7 minutes left in the first half put the Trojans up 25-17, they went nearly 5 minutes without scoring until Metu's jumper with 2:14 left — and they still led 27-24. USC was up 30-27 at the half after a late 3-pointer by Jonah Mathews.