United announced the news via their official Twitter account, saying: "Javier Hernandez has completed a permanent move to Bayer Leverkusen. We wish him all the best for the future."
The fee Leverkusen will pay, while undisclosed at the moment, is thought to be around £9million.
The Mexican striker joined United from Guadalajara in 2011 and scored 59 goals in 157 games for the club.
During his five-year spell at Old Trafford, he won two Premier League titles.
Javier Hernandez has completed a permanent move to Bayer Leverkusen. We wish him all the best for the future. #mufcpic.twitter.com/uGUMobMLzW
The 27-year-old spent last season on loan at Real Madrid and has fallen down the pecking order since the arrival of manager Louis van Gaal.
United now have a shortage of strikers, with Wayne Rooney and James Wilson now the only out-and-out forwards left on the books.
GETTY
Javier Hernandez has left Manchester United after five years to sign for Bayer Leverkusen
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Wilson is understood to be leaving as well and West Brom could take the youngster on a season-long loan.