The Tigers stranded 12 runners on base and five Auburn pitchers surrendered 14 hits to the visitors from Mobile.
Auburn coach John Pawlowski had a lengthy meeting in left field with his team following the loss. "Certainly our team is very, very disappointed with the overall effort," he said.
Pawlowski, whose Tigers had a five-game winning streak snapped on Sunday at LSU, said, "We feel like we are making progress sometimes and then we take a little step back. In the big picture we have a lot of work to do.
The Tigers surrendered six of the seven runs with two outs and did not hit well with two outs and runners on the bases.
"I didn't like our approach at the plate," Pawlowski said. "I told our team we just didn't have a good approach and consequently it hurt us. I thought we hit some fly balls. I thought we had a chance to score some runs and we left the (strike) zone a little bit. I thought we should have taken advantage of the short game more than we did and put more pressure on them."
The news wasn't all bad for the Tigers on Tuesday night. Pawlowski said Auburn's top starting pitcher, Derek Varnadore, should be ready to play this week after being held out last week with a sore arm that feels good again.
"We made some mistakes pitching-wise," Pawlowski said of the loss to South Alabama. "It was a tough lesson to learn. Our guys have to be able to flush this out pretty quick and be ready to go on Thursday."
It was a second straight loss for the Tigers, who fell to 20-16 going into Thursby night's SEC home game vs. Ole Miss to open a three-game series that concludes on Saturday.
South Alabama extended its winning streak to six games and improved its overall record to 21-16 for retiring coach Steve Kittrell, a long-time fixture at his school.
The visitors scored a run in the first inning with Nolan Early doubling to right center field with two outs and reaching home on a single by Jordan Patterson.
Bobby Andrews opened the bottom of the first inning with a bunt single despite the third baseman playing shallow expecting it. However, No. 2 hitter Cullen Wacker popped up his bunt attempt leading to a double play, foreshadowing the type of night it would be for the Tigers.
Back-to-back walks for Dan Gamache and Tony Caldwell allowed a sacrifice bunt by Wes Gilmer to put a pair of runners in scoring position with one out in the bottom of the second inning for the Tigers.
Kevin Patterson then tied the game with a line drive single to center that scored Gamache and left runners on the corners.
Justin Fradejas then hit a hard grounder to third base. The Jags got the runner at second base for out two leaving Tigers on the corners for freshman shortstop Zach Alvord, who ended the inning with a fly to center field.
The Jaguars regained the lead in the top of the third inning and chased Auburn starter Bradley Hendrix, who left the game with two outs and a runner on third. Sean Ray gave up a line drive single to left to Brent Tanner to score a run, but the lefty pitcher got out of the inning without allowing further damage.
In the fourth inning the Tigers stranded runners on second and third when Andrews hit a fly out to center field leaving Patterson on third and Alvord, who doubled off the Green Monster, stuck on second base.
Ray was pulled in the top of the fifth inning after giving up a double and walk. Ethan Wallen inherited runners on first and third with one out and gave up a three-run homer with two outs to Brad Hook, who smacked the ball over the right-center field wall to make the score 5-1.
Slade Smith came on to pitch in the sixth inning and struggled also. He immediately gave up two runs allowing the visitors to stretch the lead to 7-1. Smith then hit the first two batters in the seventh inning before being pulled for Andrew Morris, who got out of the inning with no more damage being done with the help of a groundout double play.
One of the few bright spots for the Tigers was the relief pitching of Morris, who kept the Jaguars from scoring any additional runs.