Paul Dickens earned the win for second-seeded Baylor (34-15). He gave up six hits and struck out six in 6 1/3 innings.
Tanner Tredaway and Brady Lindsly both had three hits for seventh-seeded Oklahoma (33-22).
Shea Langeliers hit a two-run homer in the bottom of the first inning and Thomas hit a two-run blast in the fourth to put Baylor up 4-0.
Baylor added three runs in the bottom of the sixth, highlighted by RBI singles from Thomas and Nick Loftin.
Oklahoma finally got on the board with a solo homer by Conor McKenna in the seventh, and Lindsly had an RBI double in the eighth.
Cade Cavalli took the loss for Oklahoma. He pitched five innings and allowed four runs.
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