The Tigers, who are 39-17-1, will now await a bid to the NCAA Tournament that will be announced on Sunday. Alabama, which lost to Auburn 6-2 in the previous meeting this year, improved to 45-10.
"We didn't play well enough to win," Coach Clint Myers said. "We beat ourselves on a few different fronts. We have to play better if we want to continue playing through the NCAA Tournament.
"With the playoffs starting, we're going to be playing teams like Alabama every time from here on out so we have to play better," Auburn's first-year coach added.
Auburn out-hit the Tide 8-7, but committed two errors while the Tiger pitchers struggled with their control.
The Tigers took a 1-0 lead in the top of the first inning as Morgan Estell scored on a single by Jade Rhodes, but the Tide matched the run in the bottom half of the inning with an unearned run on an error.
Auburn jumped in front 4-1 in the second inning on a two-run homer to Emily Carosone and a solo home run by Kasey Cooper.
However, Alabama took the lead with four runs in the bottom half of the inning and Auburn couldn't score again vs. pitcher Jacklyn Traina.
Marcy Harper (17-5) suffered the pitching loss for the Tigers. She gave up seven runs in three innings, but only four were earned.
Alabama will play Georgia in Friday's semi-finals.