Playmaker Havertz, 17, burst into the Leverkusen first team last October and has made eight 16 Bundesliga appearances this season, providing three assists, but the club announced on Tuesday that he had been left out of the trip to Atletico.
"Havertz has important exams at school," said a squad update from the club's Twitter account on Tuesday.
Leverkusen, Champions League finalists in 2002, trail Atletico 4-2 from the first leg and are without a win in their last four games in all competitions. They are 10th in the Bundesliga.
They halted a run of three straight defeats on Saturday with a 1-1 draw at home to Werder Bremen, their first game since coach Roger Schmidt was sacked. He has been replaced by Tayfun Korkut until the end of the season.
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(Reporting by Richard Martin; Editing by Ken Ferris)
