Junior Sherell Hobbs' shot would have completed a big rally for the Tigers, who trailed by 16 points in the second half as St. Joe's held on for a 71-69 victory.
Auburn got the ball back on its own baseline with two seconds left after an in-bounds violation was called on the Hawks, who had gotten the ball on a turnover by AU freshman guard Alli Smalley.
Leading the charge for the Tigers, who fell to 12-2, was junior DeWanna Bonner. She scored 30 points, one off her career high, and added a career-best 19 rebounds. Bonner made 9-21 field goals and 11-16 foul shots.
Bonner was joined on the all-tournament team by Smalley, who scored 13 points for the Tigers. Hobbs added a dozen points for the Tigers and Jordan Greenleaf chipped in with 10 rebounds.
The Hawks used strong three-point shooting to engineer the upset. They hit 10-15 three-pointers and shot 47.5 overall from the field. Auburn made 5-17 threes and 36.2 percent of its shots.
The Tigers hit 14-20 foul shots while St. Joe's made 5-9. Auburn had 10 turnovers, one less than the home team which was out-rebounded by Auburn 45-34.
"We had a chance and it was a tough loss," said Auburn coach Nell Fortner. "We fought back really hard. The free throw line wasn't good to us today. If we could have knocked down a few more free throws we could have had a shot at winning."
Auburn trailed by 16 points midway through the second half, but got back into the game with a 14-0 run. The Tigers cut the lead to 60-59 on a free throw by Smalley with 4:09 left and had multiple chances to take the lead, but couldn't pull ahead of a St. Joe's team that improved to 7-6.
Amy Wold scored 17 points and added six rebounds for the Hawks. Her teammate, Sarah Acker, scored 16 and pulled in eight rebounds.
Fortner says the Tigers needed to play with more urgency early in the game and didn't execute as well as they needed to win a the tournament in Philadelphia playing without starting point guard Whitney Boddie, who is suspended from game action due to academics. The Tigers had previously won two tournament titles on the road this year, beating Top 25 teams in the championship games.
"We started a little slow," Fortner said. "Sometimes I think they just think we are going to beat people. Sometimes that is just how kids think. Today they turned it around and got themselves back in the game."
The Tigers have five days to work on their game before returning to action with a 6 p.m. home contest on Thursday vs. No. 22 ranked George Washington.