Perry Jones III scored 18 points as the Bears upset the Jayhawks 81-72 Friday to advance to the Big 12 final.
Baylor, who had six players score in double figures, will meet Missouri or Texas in Saturday's championship game.
The Bears (27-6) will be making their second trip to the final and second in the last four seasons. They lost to Missouri in 2009 after defeating Kansas.
Baylor improved to 23-1 this season when leading at the half, but it seemed at times that trend might not hold. Baylor led 43-35 at halftime and stretched the margin as wide as 13 points before Kansas went on an 18-3 run to regain the lead.
Brady Heslip made the second of his four 3-pointers to give Baylor the lead for good a little more than a minute later and Heslip hit two more 3-pointers down the stretch to help the Bears hold on.
Pierre Jackson and Quincy Miller scored 13 points apiece while Heslip and A.J. Walton each had 12 and Quincy Acy 11 for Baylor.
Tyshawn Taylor scored 20 points for Kansas.
Cincinnati knocks off No. 2 Syracuse in Big East semifinal
Sean Kilpatrick scored 18 points - all on 3-pointers - as the Bearcats nearly blew an early 17-point lead before holding off the No. 2 Orange 71-68 in a Big East tournament semifinal thriller.
Yancy Gates added 18 points and seven rebounds for fourth-seeded Cincinnati (24-9), which will play in its first Big East championship game against Louisville or Notre Dame on Saturday.
The Bearcats scored the first seven points and stretched their lead to 25-8 when Cashmere Wright and Kilpatrick combined to hit three consecutive 3-pointers.
Syracuse (31-2) stormed back late to get within one, but denied itself a final chance at victory when Dion Waiters made a free throw that he was trying to miss with five seconds left.
Kilpatrick was 6 for 9 from 3-point range and added five assists and five steals. His final basket gave Cincinnati a 65-55 lead with 1:51 remaining.
Both teams leaned heavily on the outside shot, with Syracuse making 13 of 29 from beyond the arc while Cincinnati was 10 for 22.
Waiters came off the bench to score a game-high 28 points, including seven 3-pointers, for the Orange.