The scores were 7-6 (9-7), 3-6, 7-6.
It was Bondarenko's first tournament victory on the women's tennis tour.
She won it despite being the event's 12th seed and by taking advantage of Wickmayer's injured right knee, which occurred in the second set.
"It's feels great," the 21-year-old Bondarenko said. "I finally I have my own title (but) I didn't expect my first one to come on grass."
Bondarenko's victory was worth $31,000.
Wickmayer, 18, competed in her first career final.
"Even though my knee hurt a lot, I kept on fighting," Wickmayer said. "I'm not a quitter."