The animals were part of Barry Christmas Story at St Mary's Church on Holton Road.
The Church in Wales apologised and said it acted swiftly after Thursday's bite.
A spokeswoman added: "As generations of Barry children have learnt from riding donkeys on the local beach they are among the more stubborn and unpredictable of God's creatures."
This comes after the church was criticised for using live donkeys in a Cardiff nativity scene, with animal welfare campaigners calling it "Victorian-style exploitation".
Speaking about the bite, the church spokeswoman said donkeys played "a crucial role in the nativity story and are a very popular addition to other church events throughout the year".
She added: "We would remind children to treat all donkeys with care and respect and ask families to keep a watchful eye on younger children in particular when in the company of these much loved animals."
Donkeys have been taken away from a Vale of Glamorgan church nativity show after a child was bitten.