Striker Danny Welbeck had to drop out of the starting XI through illness during the warm-up.
His place is taken by Olivier Giroud, who suffered with thigh pain during Saturday’s 3-1 defeat at Liverpool.
Alex Iwobi also misses out through illness.
His place is taken on the bench by Mesut Ozil though the German was rated unlikely to feature by Arsene Wenger on Tuesday.
With Welbeck also ill, it leaves Wenger with a de facto five man bench.
Wenger's problems were not confined to the pitch, as hundreds of supporters gathered to demand the Arsenal board withdraw their offer of a new contract for the manager.
Around 300 fans had convened outside what was once the East Stand at their former ground Highbury an hour before kick-off, they were then set to march to the Emirates ahead of a game in which Arsenal, trailing 5-1 from the first leg, have little chance of qualification.
Wenger has been offered a two-year deal but is yet to decide whether to extend his over two decade spell at Arsenal.