The Germany international was injured in the opening seconds of Saturday's Bundesliga game against Hamburg SV, sustaining an adductor muscle tear in his right leg.
"Following extensive checks and consultations, Karim Bellarabi and Bayer Leverkusen have decided for the player to undergo surgery," the club said in a statement.
"The 26-year-old international will not be available for the rest of 2016."
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The player will miss the entire Champions League group stage.
(Reporting by Karolos Grohmann, editing by Pritha Sarkar)
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