The Wildcats (4-1) scored two touchdowns in the final seven minutes of regulation along with the overtime touchdown to avoid a stunning upset.
Eastern Kentucky (2-2) held a 27-13 lead with 7:39 remaining, but JoJo Kemp's 7-yard TD run with 4:59 remaining, followed by Towles' 5-yard touchdown pass to Dorian Baker with 52 seconds left in regulation tied the score at 27.
The Colonels got the ball back and ran out the clock, forcing the extra period.
The momentum carried over into overtime for the Wildcats. Towles' 3-yard pass to Baker on Kentucky's first series of the extra period gave the Wildcats the touchdown they needed to avoid the upset. The Wildcats stopped Eastern Kentucky on four downs to end the contest.