The pitching ran out, the bats went cold and the season ended.

Houston bashed LSU 12-2 at Alex Box Stadium on Monday night to win the NCAA tournament’s Baton Rouge regional, accomplishing a feat just two other teams had and exposing the Tigers’ flaws for the final time in 2014.

LSU (46-16-1) lost a regional at home after winning the first two games for the first time in program history. The Tigers dropped a regional in Baton Rouge for just the fourth time in 22 chances.

This one wasn’t pretty — a stunning result from a Houston team playing its fifth game in 72 hours against the tournament’s No. 8 seed.

“It’s a tough one to take,” coach Paul Mainieri said. “Today was just … just a very tough night for us all. It was awful that we had to have our worst game of the year on this date, but it is the way the game is.”

The Cougars (48-16) scored seven runs in a nightmarish third inning against LSU relievers, and the Tigers blew an early 2-0 lead to lose by the biggest margin in a regional game in 22 years.

Houston won its third game in about 30 hours, storming back from the losers’ bracket to join Rice and Cal State Fullerton as the only two non-LSU squads to win regionals at Alex Box Stadium.

“I thought this team was one of the best teams in the country,” shortstop Alex Bregman said. “Right up there with last year’s team. Just didn’t fall our way today. It’s the game of baseball. It’s about failure. You got to get back up and keep fighting.”

The Cougars squashed an LSU team that has thrived in elimination games in these confines, beating the Tigers for a second time in 24 hours and sending half of the 9,032 at the Box to the exits before the eighth inning.

Houston came back to beat LSU 5-4 in 11 innings Sunday night to send the regional to a decisive game Monday.

The Tigers led 4-0 entering the eighth inning in that one, a victory that if secured would have sent them to a home super regional against Texas. They were six outs from advancing.

“We were 2-0 in the tournament, seemingly in the driver’s seat with a 4-0 lead in the eighth inning,” Mainieri said. “We just didn’t get it done when we needed to.”

Instead, LSU’s problems surfaced in the losses Sunday and Monday.

The bullpen couldn’t hack it.

Playing a fourth game in four days, the Tigers scraped the bottom of a pitching staff that included just 12 healthy hurlers entering the weekend.

A No. 2 seed with an RPI of 10, Houston smoked the bullpen for seven runs and five hits in the third inning, and the Cougars finished with 12 hits.

Every Houston starter scored a run, and eight of them had at least a hit. UH’s seven runs in the third were the most scored against LSU this season. The Tigers had allowed seven in a game just six times before this one.

“It was as poorly a game as we pitched all year,” Mainieri said.

Houston had five hits and batted 12 men in the third, and the Tigers used three pitchers in what was a 30-minute half-inning that Mainieri called “nightmarish.”

Brady Domangue, Parker Bugg and Nate Fury all pitched.

The inning unfolded in horrible fashion for Bugg, a 6-foot-6 right-handed freshman from California. He walked the leadoff man, allowed a single and then hit the next batter. Bugg got a putout at home before hitting Landon Appling near the helmet to score a run.

Mainieri pulled Bugg for Domangue. Domangue, making his first appearance in more than a month, did not record an out while facing five batters. He allowed four hits and issued an intentional walk.

Fury worked a solid 3.1 innings, allowing just three hits, but an inexperienced and young group of pitchers — starter Alden Cartwright, Bugg and Domangue — gave up too much.

Cartwright did not record an out. He loaded the bases, hitting his first batter and then walking two before being yanked.

The bats cooled, too.

LSU went hitless for five straight innings — from the third through the seventh — against Houston reliever Jared Robinson, who threw 91 pitches in a Friday start against Bryant.

What was Robinson throwing to fool LSU?

“Splitters,” outfielder Sean McMullen said. “Just dropped off the table. Really good pitch.”

Robinson struck out eight in his lengthy stay on the mound, putting a gruesome end to an LSU season that looked so good just days ago.

LSU entered Sunday night’s game against Houston having won 10 straight and claiming the SEC tournament title during a wild season-ending run. It got the Tigers a national seed, but they ended up with the toughie of the draws.

According to cumulative RPI of the Nos. 2-4 seeds, LSU’s regional was the second-toughest nationally. Houston’s RPI was just a notch above LSU’s final ranking.

The Cougars gave LSU the worst NCAA tournament loss in Mainieri’s eight years and the worst NCAA regional loss for the program since an 11-0 loss to Cal State Fullerton in 1992.

It was an ugly goodbye for a host of players — particularly ace Aaron Nola, who’s expected to forgo his senior season and jump to the pros.

“We’re going to huddle up, say goodbye to each other,” Mainieri said, “and look forward.”

Follow Ross Dellenger on Twitter @DellengerAdv. For more coverage of LSU baseball, follow our Line Drives blog.