The club said Wendell tore a ligament in his left ankle and would undergo surgery on Wednesday.
The talented 22-year-old left back had played in 28 of their 31 league matches this season as Leverkusen climbed to third in the table, five points ahead of Hertha Berlin in fourth.
They take on Hertha on Saturday and a win would secure an automatic place in the Champions League's group stage next season.
(Reporting by Karolos Grohmann; Editing by Toby Davis)
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