Besiktas already faces a massive hill to climb after losing to Bayern 5-0 in the first leg.
Besiktas and Portugal center back Pepe will miss three weeks of action, having suffered a broken toe.
The announcement was made by UEFA's Twitter account, who report that the player won't be available to face Bayern Munich in the Champions League on March 14.
Besiktas already suffered a heavy defeat at the hands of the German giants when the two sides met in the first leg of their round-of-16 tie last month. Thomas Muller and Robert Lewandowski both recorded braces, while Kingsley Coman chipped in with a goal of his own to give the Bavarians a 5-0 advantage on their home turf.
There was very little chance of the Turkish outfit overturning the deficit, but things have been made a bit worse now that Pepe is unavailable for the next three weeks.
The 35-year-old joined Besiktas from Real Madrid last summer on a free transfer following a 10-year stint at the Bernabeu and has helped his new side maintain a decent position on the Super Lig table.
As things stand, they're in third place in the standings, with a game in hand on first-placed Galatasaray and second-placed Istanbul Basaksehir, trailing them both by six points.