The singer beat a strong male-dominated field to win the best alternative song award on Saturday.
After being awarded the category, Ebiye made the misogynistic comment on Instagram.
He later apologised by saying: “I made a distasteful joke about Aramide last night at the Headies. I am embarrassed by my comments, I’m profusely sorry.
“Aramide is a hardworking artist who deserves every recognition she gets by merit. I sincerely apologise and pledge that such will not repeat itself.”
In spite of his apology, many Nigerians on Twitter descended heavily on him.