Welbeck had initially been named in Arsene Wenger's starting line-up to face Bayern at Emirates Stadium, but was forced to withdraw during the warm-up as he failed to recover from illness.
His place is taken by Olivier Giroud, who suffered with thigh pain during Saturday’s 3-1 defeat at Liverpool, but Alex Iwobi's absence through illness meant the Gunners only had six players to call on from the bench.
Welbeck took to Twitter to deny reports that he had suffered a potential setback as he works towards full fitness following a long-term layoff due to a knee injury.
Welbeck wrote: "No injury, no tweak, just ill at the wrong moment. Devastated I couldn't play tonight."
No injury, no tweak, just ill at the wrong moment. Devastated I couldn't play tonight.— Danny Welbeck (@DannyWelbeck) March 7, 2017
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 the game.