Can had a 12 million euro (£9.75million) release clause effective for foreign clubs and it is reported Bayern Munich will receive £1.2million as compensation for waiving their buy-back option.
Bayer chief Michael Schade told the club's website: "Emre Can has developed very quickly at Bayer 04 Leverkusen over the past 12 month.
"We wanted to keep Emre at Leverkusen but the release clause is part of his contract.
"So we wish him all the best and lots of success in his time in the Premier League."
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