Guard Armintie Price scored the winning points with 1:08 left on a three-point play with a layup and foul shot.
Auburn got the ball back four more times, but couldn't score. The Tigers missed three treys in the final 20 seconds as they fell to 12-11 overall and 3-7 in the conference.
Ole Miss improved to 14-10 overall and 4-7 in the league as Price led the charge with 19 points, 11 rebounds, eight assists and six steals.
Freshman Sherell Hobbs came off the bench for a career-high 17 points for the Tigers. The forward from Huntsville hit 7-19 field goals and added 11 rebounds.
Freshman center KeKe Carrier contributed 15 points and seven rebounds for Auburn in just 22 minutes. She sat most of the first half after getting into early foul trouble.
Freshman guard DeWanna Bonner scored 10 points and contributed 11 rebounds for Auburn. AU got eight points from sophomore reserve forward Alexis Ogubie.
Chantelle Blakely made her first SEC start at point guard in place of another freshman, Whitney Boddie, who was suspended for the game by Coach Nell Fortner for violating team rules. Blakely took just one shot and did not score. She had one assist, three turnovers and one block in 33 minutes of action.
Boddie, who was Miss Basketball in the state last season as a high school senior, has been suspended indefinitely from the team, AU officials announced. They added her situation will "be re-evaluated in the coming weeks."
Auburn shot 40.3 percent from the field and 11-17 at the free throw line. The Tigers took just four three-pointers in the game and did not make any.
Ole Miss made 40 percent of its shots from the field and hit 11-14 free throws and 5-17 three-pointers.
Auburn enjoyed a 45-32 rebounding margin, but committed 21 turnovers, six more than the home team.
"I thought the effort in the second half was good," Fortner said. "We just didn't play well enough after we dug ourselves a hole in the first half. It's just unfortunate to lose today and it is a tough one to swallow."
Auburn led 18-17 with 10:32 left in the first half before the Lady Rebels outscored the visitors 14-3.
Hobbs changed the momentum with a layup at the 2:54 mark and she added three more baskets before intermission to cut the lead to 37-33 at halftime.
Hobbs tied the game with 16:11 to play on a layup and the Tigers moved ahead on a pair of free throws by Carrier. AU increased the margin to 56-50 with 7:32 to play on a basket by Bonner, but trailed again 59-58 with 5:14 to play and managed to score just three more points the rest of the contest.
Auburn returns to action with an 8 p.m. tipoff at home on Thursday vs. South Carolina.