Revd Susan Lancaster, 67, was discovered in the Moortown area of the city after a man called officers to say she was dead.
It's thought the man who made the call was her husband, Roy Lancaster, 54, who was later found dead. Police say his death is not suspicious.
Detective Chief Inspector Jim Dunkerley, from West Yorkshire Police, said: "Our enquiries are still at an early stage but we are treating the woman's death as murder.
"We are not looking for anyone else in connection with this incident."
Revd Lancaster is understood to be an associate priest at St Edmund's Church in Roundhay.
Police have searched the couple's home and are carrying out door to door enquiries but are not looking for any suspects.