The Rebels ended a three-game losing streak but shot just 34.1 percent against the Mustangs, who arrived in Oxford with a handful of close losses and a 251 RPI as well.
Holloway, the third-leading rebounder in the SEC, hasn't played since sustaining a severe ankle sprain in a 68-56 loss to Middle Tennessee State on Dec. 21.
It was against MTSU in Southaven that freshman guard Jelan Kendrick, a Memphis transfer and a McDonald's All-American, played 29 minutes in only his second appearance.
But Kendrick's minutes declined in last week's 62-50 loss and Dayton, and he did not play at all against the Mustangs (8-6) for what Ole Miss coach Andy Kennedy called a "coach's decision." It's the second time Kendrick has missed a game for that reason.
Terrance Henry had 13 points to lead all scorers. He breathed a sigh of relief with the win that came after a players only meeting earlier Tuesday.
Kennedy has challenged his upperclassmen - any of them - to shoulder more of the load with Holloway out.
"After a three-game losing streak, our confidence was shot, and everybody's heads were down," he said. "We laid a lot of stuff down on the table. With Murph being out, that's a lot of production missing."
If he continues to progress, Holloway will play in the Rebels (10-4) SEC opener Saturday at LSU. Kendrick's status remains unclear.
Against the Mustangs, Ole Miss closed the first half on a 16-4 run to lead 28-21 at the half.
SMU tied it at 36 with 10 minutes, 51 seconds remaining when guard Jalen Jones knocked down a jumper on an assist from Robert Nyakundi.
The Rebels regained the lead and stretched their advantage to eight points with 7:29 to play, but Nyakunkdi, the Mustangs' leading scorer at 16 points a game, scored eight straight points in a span of 2:03 and tied the game at 44 with a 3-pointer from the corner.
The Rebels played much more zone than man defense, a move made to better keep up with SMU's shooters, Kennedy said.
The Mustangs shot 36.5 percent and missed their final two shots, 3-point attempts that would have given them the win.
The first look was the best, a called play with 11.6 seconds left after Henry's two free throws put the Rebels ahead 50-48.
SMU guard Aliaksei Patsevich threw the ball in-bounds from the side, then stepped in and took the pass before the defense could close in. He got a clean look but missed the shot.
"Fourteen games into the season, and we're still having so many inefficiencies, passing, catching and dribbling, which are important qualities to be a Division I basketball player," Kennedy said. "We have a saying with this team, 'embrace the grind.' It's going to be a grind, so just hang on with both hands. It's who we are."