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All contestants in Muslimah World must wear the hijab Ms Ajibola, 21, cried and recited a verse from the Koran when her name was called as the winner. She was awarded 25m rupiah ($2,200, £1,360) and trips to Mecca and India.
She had said in an interview before she won that she was just trying "to show the world that Islam is beautiful".
Eka Shanti, who lost her job as a TV news presenter for refusing to remove her headscarf, started the pageant three years ago.
She told Agence France-Presse news agency they held the pageant days before the Miss World final "to show that there are alternative role models for Muslim women".
"But it's about more than Miss World. Muslim women are increasingly working in the entertainment industry in a intercourseually explicit way, and they become role models, which is a concern," she said.
Indonesia is the world's most populous Islamic country.
The Miss World grand final had been scheduled for 28 September at a venue near Jakarta, but is now being held in Hindu-majority Bali after strong protests by Islamic groups.
Miss World organisers have criticised the Indonesian government for not supporting the event.
BBC