The official spoke to The Associated Press on Tuesday on the condition of anonymity because the decision was not to be announced until a news conference at noon.
Skinner just finished his 13th season guiding the Eagles. He was the winningest coach in school history, with a 247-165 record and seven NCAA tournament berths since 2001.
The official said the decision had been made before Skinner was been given permission to interview for the St. John's job.
Skinner's departure was first reported by The Boston Globe.