The win snapped a two-game losing streak for the Rebels (15-9, 5-5 Southeastern Conference) as Nick Williams and Jarvis Summers added 13 and 11 points, respectively.
Holloway also grabbed 10 rebounds as Ole Miss erased an 11-point deficit in the final 15 minutes to keep alive its NCAA Tournament hopes.
Auburn (13-12, 3-8) was led by Kenny Gabriel with 15 points. Frankie Sullivan added 10 for the Tigers, who have lost five of their last six and remain winless in six SEC road games.
The Tigers led 31-24 at halftime and 39-28 with 15:16 left on a 3-pointer from Noel Johnson. Ole Miss answered with 12 straight by Holloway to lead 40-39.
With the game tied at 51, the Rebels outscored the Tigers 10-3 in the final 2 minutes.
Auburn finished 21 of 52 (40.4 percent), from the field, including 6 of 17 (35.3 percent), from 3-point range. Ole Miss shot 22 of 49 (44.9 percent), but struggled at the free throw line, making 13 of 25 (52 percent), which allowed the Tigers to make it close.
Holloway, who finished with a game-high 10 rebounds, highlighted his decisive outburst with a traditional three-point play and a thunderous dunk.
The teams swapped the lead on three more occasions before the Rebels took the lead for good, 53-51, on a steal and layup by Summers with 1:56 left.
Auburn managed only one field goal in the final 2 minutes, a 3-pointer by Gabriel, as Ole Miss pulled away on baskets and free throws from Summers and Williams.
Reggie Buckner, who finished with four blocked shots, had three blocks in the final minute and added a basket to complete the comeback win.
The win enhanced the NCAA Tournament hopes of the Rebels, who remain in a four-team logjam for fourth place in the SEC at 5-5. Ole Miss hosts Vanderbilt on Thursday and visits Kentucky on Saturday in a pair of games that should determine the Rebels’ postseason position.