The No. 6 Jayhawks shook off an early deficit to earn a chance against Kansas State in the championship game Saturday.
No. 12 Kansas State, which shared the regular-season league title with Kansas, reached the finals thanks to a 68-57 victory over Oklahoma State.
Ellis hit 10-of-12 from the field and was the key ingredient in Kansas extending what had been a four-point halftime lead.
Jeff Withey and Elijah Johnson both scored 14 points for Kansas (28-5), which shared the regular-season crown with Kansas State.
Kansas defeated Iowa State for the 16th time in 17 meetings.
Iowa State owned as much as an eight-point lead early in the first half, but Kansas went on an 8-0 run to get back in the game and had a 35-31 advantage at intermission.
Georges Niang scored 19 points for Iowa State (22-11), which came into the contest on a three-game winning streak.
Kansas shot 69 percent in the second half while piling up 53 points.
Rodney McGruder came through with 25 points in the win for Kansas State (27-6). The Wildcats slowly pulled away in the second half in a defensive duel that saw Oklahoma State hit just 30 percent of its field goal attempts.
Kansas won both its meetings with Kansas State, downing the Wildcats by 21 on the Jayhawks' home floor.