The Rebels (9-2) rallied from a 13-point deficit in the first half to advance to Tuesday's fifth-place game.
Holloway, a senior forward, was 9 of 15 from the field and made 5 of 7 free throws. He had 16 points and 13 rebounds on Saturday in the Rebels' 87-85 overtime loss to Indiana State.
Nick Williams scored 18 points, making 4 of 7 from 3-point range. Marshall Henderson scored 12 and Jarvis Summers added 11 points for Ole Miss, which made 9 of 19 from 3-point range.
San Francisco (5-6) shot 60.7 percent from the field in the first half, but just 40.7 percent after halftime. Cody Doolin led the Dons with 20 points, seven rebounds and eight assists.
De'End Parker had 17 points and Cole Dickerson scored 14 for San Francisco.
San Francisco led 32-19 with 6:17 left in the first half following Doolin's 3-pointer, but the Rebels used a 14-4 run to cut it to 36-33 with 2:20 left until halftime. It was 38-33 Dons at the half.
The Rebels took the lead for good at 64-62 with about seven minutes to play on Williams' 3-pointer. It was part of a quick 8-0 Ole Miss run in less than a minute that turned a 62-58 deficit into a 66-62 advantage.
The Rebels shot 52 percent from the field in the second half and made 24 of 30 free throws, including 20 of 24 after the intermission. Ole Miss overcame 14 turnovers against just five assists.
San Francisco lost to No. 18 San Diego State 80-58 on Saturday.
Rebels junior center DeMarco Cox exited the game near the midpoint of the first half with an apparent left ankle injury. He was helped off the court and into the locker room and did not return. His status for Tuesday is uncertain.