The 26-year-old has been an ever-present for Sami Hyypia's charges this season, helping the club to third place in the Bundesliga standings.
But he will now miss the Olympiastadion clash, with 19-year-old Greece international Kostas Stafylidis set to deputise in his absence.
Poland defender Boenisch signed for Leverkusen in November 2012 and has since made 36 appearances for the club, helping them to a top-three Bundesliga finish last term and UEFA Champions League qualification.
Sami Hyypia's side have enjoyed a terrific start to the campaign, taking 28 points from 12 league fixtures, and trail leaders Bayern Munich by just four points.
They resume their domestic campaign against Hertha, and will look to build on a 3-2 success at Hoffenheim before the international break.
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