The France international was not risked in Saturday's 3-2 defeat to Stoke City, having suffered with the niggling injury throughout the course of the season.
Following an eight-week absence, the centre-back played against Southampton and West Brom in quick succession, but will not be risked in Tuesday's Group D clash.
Arsene Wenger has already confirmed Alexis Sanchez will not travel to Istanbul, with Arsenal guaranteed progression.
"A few players [will not travel] because there's not a lot at stake and we have given a lot in the last two weeks," Wenger said.
"We have to recover a little bit. Alexis will not travel and I don't think I can play, for example, Koscielny.
"[Koscielny] didn't play on Saturday and I don't see why I should risk him for a game where’s there's not a lot at stake - first place hypothetically, but there’s maybe a 10 per cent chance."
Arsenal will top the group with a win if Dortmund lose to Anderlecht or, if the Bundesliga side draw, then Wenger's men will need to win by a big enough margin to overtake Jurgen Klopp's charges on goal difference or goals scored.
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