Southern Miss will not repeat as Conference USA Tournament champions.
The Golden Eagles, the second seed, dropped a 7-6 14-inning decision to sixth-seeded Houston early Friday morning at Trustmark Park in Pearl.
The loss likely cost Southern Miss a shot at hosting a regional for the first time since 2003.
Houston won the game in the bottom of the 14th on an old-fashioned squeeze play that saw Ryan Still score John Cannon with the perfectly executed bunt off Southern Miss closer Collin Cargill.
The game lasted 4:43 and ended at 1:50 a.m.
By virtue of the win and an opening-day victory over East Carolina in Pod 2 play, the Cougars will play for the tournament championship on Saturday against Pod 1 winner (Rice or Central Florida) and an automatic berth into the NCAA Tournament.
Southern Miss (39-16) and East Carolina (38-19) will close out Pod 2 play today in a meaningless game at 7:30 p.m. The Cougars (27-30) play Tulane at 4 p.m.
Houston, which beat Southern Miss four times in five meetings this season, took a 1-0 lead off former St. Stanislaus standout Boomer Scarborough in the third inning.
Cody Morehouse led off that inning with a single to right before taking second on a sacrifice and third on a passed ball. Scarborough then walked Ryan Still to put runners on the corners. A pickoff attempt at first base was wild, scoring Morehouse.
In the fifth, Scarborough gave up a single and walked two to load the bases before being lifted for Chase Horn with two outs. M.P. Cokinos greeted Horn with a two-run single to left and Houston led 3-0.
Southern Miss got to Wiley with three earned runs off two hits -- the big blow being a double by Kameron Brunty.
Graeter was credited with an RBI with a fly out and Bourgeois added an RBI with a single to left and Isaac Rodriguez closed out the scoring with an RBI goundout to score B.A. Vollmuth of Biloxi, who was hit by a pitch.
Houston then regained a 5-3 lead only to see Southern Miss come back with three runs in the eighth that included a Marc Bourgeois two-run single.
Houston forced extra innings with a run in the ninth off Cargill, who threw 98 pitches in 5.2 innings of work.
With the game tied at 6-6 in the 11th, Southern Miss failed to score when Brunty lined a Morehouse fastball off the rightfield wall. Brunty was thrown out at the plate with no outs trying to turn a triple into an inside the park home run.