Rico Gathers came off the bench to pop in 14 points for the Bears (14-7, 2-6 Big 12).
Cory Jefferson had 11 points and 13 rebounds and Gary Franklin scored 11 for Baylor.
Markel Brown scored 24 points, Le'Bryan Nash added 19 and Marcus Smart contributed 15 for the Cowboys (16-5, 4-4), who dropped a second straight.
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