The Bears scored six runs over the first two innings, but KU starter Doug Lantz settled down, striking out a career-high 10 batters, and held Baylor to one run the rest of the way.
Regardless, the Bears completed the three-game weekend sweep with a 7-4 victory.
"That's a tremendous job of battling and competitiveness and I told our pitchers it's a lesson to be learned," KU coach Bobby Randall said. "Who thought he would go nine (innings)? Doug. The only person in the ballpark who thought he would go nine is Doug Lantz. He put it together and I was proud of him.
"He was real flat early but I think it took him a little bit to get the pitches to where he wanted to. He was up in that first inning. But other than that I don't think you can fault anything else he did."
Randall was pleased the Jayhawks finally played a close game with the 16th-ranked Bears. Baylor won the first two games by a combined score of 23-2.
"I thought our bats battled a little bit better than they did the first two days," Randall said. "I liked what we did better today and I'm proud of what our team did. I never, never compromise on the fact that we're trying to win the game so we're not going to accept losing, but the effort and the way we played was a lot better."
Baylor (21-8 overall, 9-3 Big 12 Conference) scored its first-inning runs on a double by Kelly Shoppach, a single by Paul Richmond and a three-run homer by Matt Williams.
Trevor Mote drove in Matt Saccomanno with a sacrifice fly in the top of the second for a 6-0 lead, but KU scored two runs in the bottom half of the inning on a home run by Ryan Klocksien.
"I was just thinking, 'First-pitch fastball,' and he threw it down and I just drove it over the 375 sign," Klocksien said.
The Jayhawks (14-14, 2-10) closed within two runs in the bottom of the eighth inning on Klocksien's double that drove home Casey Spanish and John Nelson.
Klocksien finished 4-for-4 with four RBIs, raising his average to .313.
"I've just been staying back and swinging at the pitches I can drive," he said. "I'm not swinging at balls out of the strike zone as much as I used to and I'm driving the ball."
Baylor scored its final run in the top of the ninth on a double by David Murphy. KU put two runners on base in the bottom of the inning, but Nelson struck out looking to end the game.
"We made a run, but it wasn't the ninth inning that hurt us," Randall said. "We wasted a couple of opportunities early in the game and we needed some more runs."
While he wasn't happy with the team's wasted opportunities, Randall was pleased with the Jayhawks' effort.
"Yesterday we didn't show up and I was disappointed in that," he said. "Today, that was more like the baseball team that we have and that's what I expect. That's more of a winning effort, but it's just not a winning result. If we play that kind of baseball every day, better things are going to happen."
KU will travel to Fayetteville, Ark., on Tuesday to face the Arkansas.
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