The Crimson Tide's 42-game winning streak when scoring 10 or more runs was also snapped with the loss to the Tigers, who have beaten the Crimson Tide 12 times in the last 14 meetings.
Alabama (20-7, 5-4 SEC) trailed 11-2 in the entering the bottom of the seventh inning but scored four runs in the seventh and four more in a wild ninth inning.
Trailing 11-6 entering the final inning, Alabama put seven straight men on base and had the winning run on second base when the game came to end.
Facing right-hander Billy Sadler, senior centerfielder Travis Garner, who had three hits and scored three runs, started the rally with a walk and moved to second on Allen Rice's single to left field. Adam Pavkovich the lined a single to right field, loading the bases with one out.
Beau Hearod then reached on an error when his ground ball went through the legs of first baseman Clay Harris, scoring two Garner and Rice to cut the lead to 11-8. Pavkovich made it a two-run game as he scored on Matt Liuzza's passed ball.
After the error by Harris at first, Sadler then walked Zac Welch and Nathan Meiners to re-load the bases.
Right-hander Justin Meier came on in relief of Sadler and hit Al Hecklinski with his first pitch, forcing home Hearod from third base as UA cut the lead to 11-10.
But that was a close as Bama would get, Meier then struck out Grant Redding with a called third strike and catcher Bobby Burns fouled out to the Liuzza behind the plate on the first pitch as Meier earned his first save of the season.
"It happened so fast," Garner said, who extended his hitting streak to 17 games with a third inning double. "We battled back and thought we were going to win the game and then four pitches later the game is over. It was a tough loss."
The Crimson Tide gave itself a chance at a ninth-inning rally as they scored four times of starter Nate Bumstead in the seventh inning, turning a blowout loss into a chance to win the game.
Pavkovich drilled a two-out single to left field, scoring Garner and Rice, and Hearod followed with a two-run home run to left. Hearod's league-leading 11th home run of the year trimmed the LSU lead to 11-6.
In addition to Garner, Pavkovich also had three hits for the Crimson Tide in the losing cause. Hearod led the way with three RBI.
Bumstead (3-1) worked seven innings and allowed six runs and eight hits for the win. He added two walks, six strikeouts and three wild pitches.
The Tigers hit a season-high four home runs, which helped them to an 11-2 lead after six innings.
LSU (18-9-1, 7-1-1 SEC) broke snapped a 2-2 tie with a solo home run from Clay Harris to lead off the third inning. Then the Tigers broke the game open with four runs in the fifth inning and added four more runs in the sixth inning.
The Tigers hit two home runs in the fifth inning, a two-run shot by Ivan Naccarata and a solo blast by Harris, his second in as many innings.
Naccarata's fifth home run of the season chased losing pitcher Allen Ponder (2-2), who was charged with five runs and eight hits in four plus innings.
Harris' second home run of the game came off Brian Reed, who also allowed an two-out single to Matt Liuzza to cap the scoring in the fifth.
The Tigers put together another two-out rally in the sixth inning, scoring four more runs off Reed. Ryan Patterson drove in two runs with a single to center and Jon Zeringue followed with a long home run to left field, scoring two more runs.
Reed yielded six runs and nine hits, both career highs, in five innings of relief work for the Crimson Tide. He also added five strikeouts.
Naccarata, Harris and Patterson all had three hits and two RBI to lead the Tigers' 17-hit attack. Zeringue and Liuzza had two hits each.
LSU took a 2-0 lead in the first inning on Blake Gill's two-out, two-run double. The double was his third hit and seventh RBI in the series with two outs.
Alabama scored single runs in the first and third innings to tie the game at 2-2. Rice walked and scored on a wild pitch in the first inning to cut the lead in half. Garner doubled and later scored on Pavkovich's sacrifice fly to right field, tying the game at 2-2 after three innings.
The three-game series, which included standing-room only crowds on Friday and Saturday, drew a record 19,224 fans, eclisping the previous record of 19,004 set against Miss. State in 2000.
The Tigers return home Tuesday for the first time since March 16 when they face the Nicholls State Colonels in a 6:30 p.m. game at Alex Box Stadium. LSU hosts South Carolina next weekend in SEC play.
Alabama is home Wednesday night against West Alabama for a 6:30 p.m. game. The Crimson Tide will travel to arch-rival Auburn next weekend for a three-game series on the Plains.