After Voegele exited, Baylor mounted its comeback against Kansas relievers Riane Ritter and Boede Rahe.
A two-run double from Brytton Clements and a game-tying, two-strike single by Pearson Riebock keyed the rally.
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Following the loss, Baylor head coach Mitch Thompson expressed pride in his team's resilience.
"They battled their tails off today," Thompson said. "We were down against the top-seeded team in the tournament and never say die.
We got back into it, and different guys stepped up all day long. It was awesome to see so many different guys compete."
Thompson acknowledged that while his team showed significant fight, they ultimately fell short against the regular-season conference champions.
"It was 7-1, and it wasn't looking good, and there haven't been many positives, but all of a sudden, there we go," Thompson said.
"We get four, and then it's 7-5, and we're back in it. I give our guys a lot of credit for that.
The heart and the competitive spirit are fantastic. We just didn't quite have enough.
I give credit to Kansas. They got it done, but our guys fought and competed really hard.
We got a lot to be proud of."
Rahe earned the pitching win after throwing a scoreless top of the tenth inning.
Baylor closer Caleb Bunch took the loss after yielding the decisive leadoff home run to Flowers.
Kansas will face fifth-seeded Oklahoma State in the semifinals on Friday at 6:30 p. m.
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