The 31-year-old striker scored one goal in 24 games for the Dons since arriving from West Lothian last summer. Twelve of his appearances came off the bench.
The former Arsenal player last featured on February 15, under caretaker boss Barry Robson.
Manager Goodwin last month claimed Emmanuel-Thomas was "not fit enough to play the type of football that I want us to play".
Emmanuel-Thomas follows Scott Brown and Mikey Devlin in departing the club since Goodwin took charge while the imminent exit of long-serving defender Andrew Considine was confirmed last week following a breakdown in contract talks.
An Aberdeen statement added: "All at Aberdeen FC wish Jay the very best in his future career."
The Pittodrie side are now without a fixture until Saturday, April 23 when they host Livingston in the first match following the Scottish Premiership split.