Gipson twice closed Kansas State's deficit to four points in the final 1:09, including a basket inside with 48.5 seconds left. Jevon Thomas missed on a drive after Long Beach State missed a free throw and Kansas State was forced to foul.
Jones made four free throws in the final minute to seal the win for the 49ers in front of a packed home arena. Kansas State's leading scorer, Marcus Foster, had five points on 1-for-13 shooting.
Long Beach State took a 33-26 lead into halftime, led by McKnight's eight points and Samuels' six points and six rebounds. The 49ers never trailed despite 11 turnovers and an 11-4 disadvantage on the offensive boards.
Kansas State, which averaged 40 first-half points in its first two games, shot 29 percent, including 3-for-11 from 3-point range. Foster and Gipson combined to go 1-for-7.
The 49ers took their biggest lead of the first half at 31-17 on an alley-oop dunk from Jack Williams to McKnight that energized the home crowd. Caffey got a layup off Tyler Lamb's steal that made it 33-20 before the Wildcats closed the first half on a 6-0 run, capped by Nino Williams' jumper at the buzzer.
Kansas State: The Wildcats shot better than 65 percent from the field and averaged 50 points in the second half in their first two games but were held to 37 percent and 36 points. It was Kansas State's first visit to Long Beach State since 1998.
Long Beach State: Coach Dan Monson needs two wins to pass Jerry Tarkanian for most in school history (123). Caffey needs 10 points to tie DeAnthony Langston for 13th on the school's career scoring list.
Long Beach State visits UCLA on Sunday.