Zach Graham added 13 points to become the 32nd player in school history to reach 1,000 career points.
Terrance Henry had 11 for the Rebels (12-3), who shot 69.6 percent in the second half and had a 14-0 run early in the frame.
Robert Nyakundi hit six 3-pointers and finished with 22 points for the Mustangs (9-5), who had their five-game winning streak snapped.
Ole Miss led 36-35 before Henry hit a jumper with 17:06 remaining to spark the decisive spurt, which included three acrobatic dunks, the last by Graham for a 59-39 lead with 9:22 to go.
SMU didn't get closer than 14 the rest of the way.
The Rebels trailed for most of the first half before scoring the final five points to take a 32-30 intermission lead. Ole Miss has won four straight games and nine of its last 10.
Steadman Short was 5 of 6 for 10 points and had five rebounds.
"Stead really stepped up and played well," Kennedy said. "I think he's really starting to get it. Typically it takes a junior college player about 10 to 12 games, and that's been the case with him. The last three or four games we've seen his potential."
"When I get into it, I get emotional," Short said of his efforts. "That's how I play. It hypes me up and turns up my energy. We're a guard-oriented team, but for the bigs, we need to step up and do our part. We have to do that to do some things in the SEC."
The Rebels begin Southeastern Conference play Saturday night at Florida.
"This is a good win," Kennedy said of Wednesday night's victory. "I'm proud of our effort."