Jones had 31 points and the Bears (26-6) defeated Kansas State 82-74 before Johnson's 26-point game fired the Jayhawks (27-5) to an 83-66 decision over Texas A&M.
Kansas and Baylor will meet in one of Friday's tournament semifinals. The other semifinal will send No. 5 Missouri against Texas.
The Tigers coasted to an 88-70 victory over Oklahoma State and the Longhorns pulled off a mild surprise in downing Iowa State 71-65 to enhance their chances of an NCAA Tournament berth.
Jones had a personal eight-point run over 76 seconds that turned the day's first game in Baylor's favor. He hit a 3-point shot that put the Bears ahead 16-15 and added a layup and then a 3-point play for a 21-15 Baylor lead.
The Bears pulled away from there and led by double digits much of the second half.
Jones hit 11-of-14 shots from the field and had 21 points in the first half, finishing with 31. He was one of five Bears in double figures. Brad Heslip had 15, Pierre Jackson 13, A.J. Walton 11 and Quincy Acy 10.
Kansas State (21-10) was led by Jordan Hernandez, who had 22 points.
Kansas broke open a tight game with a 15-2 run midway through the first half. Johnson had 10 points in the run that ended with a Tyshawn Taylor field goal that gave the Jayhawks a 30-21 lead.
Texas A&M (14-18) was not a factor the rest of the way. The Aggies got 24 points and Khris Middleton.
Missouri (28-4) stormed to a 25-point lead at the intermission against Oklahoma State and was able to rest its key players for Friday's meeting with Texas. Kim English had 27 points for the Tigers and Marcus Denmon scored 24.
Keiton Page led Oklahoma State (15-18) with 22.
Texas won for the seventh time in 10 games, getting 23 points from J'Covan Brown. The Longhorns (20-12) took the lead for good on two free throws by Clint Chapman with 4:22 to play that touched off a six-point run.
Royce White scored 17 points for the Cyclones (22-10).