"With this transfer we have managed to adapt our squad to the big challenges of the coming months," Leverkusen chief executive Michael Schade said in a statement on Monday.
"After qualifying for the Champions League (group stage) we wanted to set a marker and we've managed to do that with Javier Hernandez."
No fee was disclosed but media reports put it at 13 million euros ($14.57 million).
The 27-year-old Hernandez, who joined United in 2010 but spent last season on loan at Real Madrid, has signed a contract that will keep him at the Bundesliga club until 2018.
Leverkusen beat Lazio 3-1 on aggregate to qualify for the Champions League group stage where they will face Barcelona, AS Roma and BATE Borisov.
($1 = 0.8921 euros)
(Reporting by Karolos Grohmann; Editing by Tony Jimenez)
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