The Knights (1-2) trailed 7-3 late in the first quarter before ending the game with 38 straight points. It was their seventh consecutive win over the Wildcats. UCF is now 20-0 against FCS foes since moving up to FBS in 1996.
Bethune-Cookman (2-1) was trying to become the first Mid-Eastern Athletic Conference team to defeat two FBS schools in the same season.
But the Wildcats offense struggled from the second quarter on, converting on just 3 of 13 attempts on third down, and giving up six sacks. They also were plagued by a season-high 17 penalties.
UCF has a bye week before travelling to Houston on Oct. 2 to begin its American Athletic Conference schedule.
In his second straight start Holman reverted back to some of the accuracy issues that prevented him from being named the starter for the Knights season opener. But he recovered to finish 6 of 11 for 145 yards, before ending his night after three quarters.
Holman will have to get by without one of his starting receivers against Houston in two weeks, though.
Rannell Hall was ejected in the fourth quarter after being called for targeting while attempting to make a block. By rule he must miss the first half of UCF's next game.
The game kicked off with soggy conditions and a penalty on Bethune for not wearing white jerseys as the visiting team.
The conditions and atypical start affected the early gameplay, as both teams struggled to move the ball early.
But UCF survived the sloppy play and was able to take a 20-7 lead into the break.
The Knights got on the board first with an early field goal lead, before a pair of defensive penalties helped set up 1-yard touchdown run by Bethune's Danny Jordan to put the Wildcats in front 7-3.
It was short-lived momentum, as UCF defense used five first-half sacks to put the offense in better situations in the second quarter.
The five first-half sacks were season-high for the Knights.
B-CU held the ball nearly eight more minutes that the Knights in the opening 30 minutes, but were 0 for 7 on third down.