Conner Teahan added 14 and Jeff Withey had 13 points and 13 rebounds for the Jayhawks (6-2) who shot 54 percent from the field to hold off the 49ers (4-4).
Kansas had the edge in rebounding 36-24 and blocked a dozen shots.
T.J. Robinson led Long Beach State with 19 points and was one of four players in double figures.
Kansas enjoyed a comfortable 51-39 lead at halftime but the 49ers pulled to 84-80 on a 3-point shot by James Ennis with 43 seconds to play.
The final two 3-point attempts by Long Beach state missed while the Jayhawks put the game away at the free-throw line.
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