Jackson recorded 10 assists to go with 28 points as Baylor (18-13, 9-9 Big 12) earned a sixth seed in next week's Big 12 Tournament.
Jefferson, meanwhile, went 11-for-13 from the field on his way to 25 points, adding seven rebounds and three blocks.
Ben McLemore finished with 23 points for the Jayhawks (26-5, 14-4), who finished as Big 12 co-champions with Kansas State. Perry Ellis added 12 points for Kansas, which earned a share of its ninth straight conference title.
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