The 42-year-old had been in charge since the start of the 2013/14 season but had come under pressure after elimination from both the Champions League and Europa League qualifiers this term and indifferent domestic form.
"Panathinaikos FC announces the termination of its cooperation with Giannis Anastasiou by mutual consent,” said the second-placed club in a statement.
"After two-and-half years together an eventful journey has come full circle. During his time we celebrated winning the Greek Cup in 2014 and enjoyed great victories with special significance for the club and the fans."
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Anastasiou was credited with rebuilding a new-look Panathinaikos with an emphasis on young Greek players following a period of financial turmoil and was Greece’s 2014 coach of the year as his team won the Greek Cup and finished runners-up in the Super League.
But a bad start to this season was highlighted by the Greens missing out on the money-spinning Champions League group stages and domestically they have lost ground on leaders and arch rivals Olympiakos Piraeus.
Their latest poor performance was a drab goalless draw at home to AEK Athens on Sunday which saw them slip eight points adrift of top spot after only nine games.
Panathinaikos president Giannis Alafouzos added: "Giannis came in at a very difficult time for Panathinaikos in May 2013. Together we created a plan that was executed with consistency and resulted in the creation of a team that all of our fans appreciated achieved some important results.
"Mistakes were made on both sides during our cooperation and everyone at Panathinaikos would like to thank him for his contribution and wish him good luck in his career."
(Editing by Mark Meadows; mark.meadows@thomsonreuters.com; +44 20 7542 7933; Reuters Messaging:; mark.meadows.reuters.com@reuters.net)
