PSG, who were crowned Ligue 1 champions on April 15 and also won the League Cup, take on third division Les Herbiers in the French Cup final next month.
However, the club, who have won five French league titles in six years and are owned by big-spending Qatar Sports Investments, have been unable to convert their domestic dominance into success on the European stage.
Emery's team were beaten in the last-16 of the Champions League by Real Madrid this season despite breaking the world transfer record to sign Brazil striker Neymar, and were knocked out at the same stage last season by Barcelona.
Neymar was bought for 222 million euros (195 million pounds) from Barcelona in the close season to help increase PSG's chances of winning Europe's elite club competition, and Emery was widely held responsible for their disappointing Champions League campaign.
"I have communicated to the players my departure," Emery told a news conference. "I thank President Nasser Al-Khelaifi, sports director Antero Henrique, the supporters and all the players for these two seasons."
Emery said that PSG had a strong project and that their record signing Neymar wanted to "grow and grow" with the club.
"It's important to be motivated for every match, and I'm happy with the mood of the players for the end of the season," he added.
The former Sevilla manager's departure was widely expected and French and German media have reported in recent weeks that former Borussia Dortmund coach Thomas Tuchel is the frontrunner to replace him.
(Reporting by Simon Jennings in Bengaluru; Editing by Matthew Mpoke Bigg, Christian Radnedge and Toby Davis)
