Hubert piled up 101 yards on 10 carries as the Wildcats (5-0, 2-0 Big 12) went undefeated over their first five games for a second straight year.
Collin Klein passed for a pair of touchdowns and ran in two scores, carrying the ball 10 times for 116 yards to help Kansas State reel off 35 second-half points.
Travis Tannahill and Tyler Lockett each made a scoring grab in the win.
The Jayhawks (1-4, 0-2) dropped their fourth straight as Dayne Crist was picked off three times.
James Sims carried the 28 times for 115 yards and a score for Kansas.