The disease has spread across Liberia, Sierra Leone and Guinea, killing more than 4,500 people.
It spreads through direct contact with the blood or body fluids of a person after symptoms of the disease have developed.
Dr John Sentamu told the BBC: "Don't think that by not going to church because you are infected somehow there will be a bolt from the blue really smashing your head."
The archbishop said God would forgive people who stayed away from church until the virus was contained.
His comments come after a group of African bishops collectively opposed closing country borders as a way of stopping Ebola.
The Symposium of the Episcopal Conferences of Africa and Madagascar (SECAM) told Fides news agency: "The closing of borders is not the solution to Ebola."
SECAM also highlighted the continued suffering of West Africans, the need for continued medical support from other countries, and the need to be "inventive" in stopping the crisis.