Kansas State (6-4, 4-2) stayed close in the first half by forcing two fumbles and an interception by Reesing, then took over in the second behind Thomas' bruising running to end a three-game losing streak to Kansas (5-4, 1-4) in the 107th version of the Sunflower Showdown.
Reesing had another forgettable game a week after being benched, undone by early turnovers, occasionally wobbly passes and a few drops.
He finished with 241 yards on 14-of-27 passing, and Jacob Branstetter missed 30-yard field goals in each half for the Jayhawks' first four-game losing streak since 2006.
Thomas opened the game with a 20-yard run and had 105 yards in a dominating third quarter to become the ninth player in Kansas State history to eclipse 1,000 yards in a season (1,087). The junior college transfer came up with the biggest play of the game on the first drive of the second half, dashing up the middle for 40 yards to set up his 5-yard TD run to make it 17-7.
Branstetter followed with a 46-yard field goal, but Kansas State ground out the final 5:20 behind Thomas and quarterback Grant Gregory to win its ninth straight home game over Kansas under coach Bill Snyder.
Reesing was a Heisman Trophy candidate through the first five games, throwing for over 1,600 yards and 13 touchdowns with three interceptions.
His season started to come unhinged with a strained groin against Colorado, leading to seven turnovers over the next three games. A three-year starter, Reesing was benched for the first time in the fourth quarter against Texas Tech last week after being sacked six times and failing to move the offense.
It didn't get any better.
Reesing was dropped for a 12-yard loss on Kansas' first drive after Darrell Stuckey returned the opening kickoff 67 yards, then threw a nowhere-near-his-receiver interception inside Kansas State's 10-yard line on the second drive. He closed out the first quarter by doinking a side-armed shovel pass off Toben Opurum's facemask.
Midway through the second quarter, Reesing finally found a rhythm. Getting cornerback Joshua Moore to bite on a play-action fake, he threw a receiver screen to Dezmon Briscoe, who turned it into a 17-yard touchdown and a 7-3 lead.
The success was shortlived.
Reesing fumbled on the next drive, stripped from behind by Jeffrey Fitzgerald on a scramble inside the Kansas 25. Next drive, same thing: Trying to get extra yards on a scramble, Reesing had the ball jarred loose by a hard hit with 36 seconds left in the half.
Josh Cherry missed a 39-yard field goal after the first fumble, but Reesing and the Jayhawks weren't so fortunate after the second. Gregory hit Lamark Brown on a 31-yard touchdown to put the Wildcats up 10-7.