Arsenal were awarded a penalty six minutes later as Christoph Zimmerman handled from a free kick.
Arsenal flop Nicolas Pepe was consigned to the bench for Arsenal's 2-2 draw at Norwich on Sunday after failing to impress interim manager Freddie Ljungberg on the training pitch.
After falling behind, the Gunners levelled thanks to a penalty from Aubameyang.
Ljungberg would have expected his players to kick on, but like in the opening 45 minutes they retreated after levelling and Norwich squandered three huge chances in the space of four minutes.
Ljungberg - and whoever comes in as permanent manager - have a huge task on their hands to get this Arsenal team organised as we're so open in midfield and the defence has no clue how the DEFEND.
The first effort was saved by Tim Krul but VAR ordered a re-take due to encroachment and the Gabon worldwide made no mistake second time around.
Aubameyang fired home the retake, sparking a furious reaction from Norwich players and fans alike.More news: Minnesota Vikings: 3 Players that must shine vs. Seahawks, Week 13
More news: Patriotism is the theme of Christmas at the White House
More news: Avs score seven straight, rout Blackhawks in Rantanen's return
Ljungberg made five changes to the team that lost to Eintracht Frankfurt on Thursday with Mesut Ozil and Alexandre Lacazette among those recalled.
And speaking after the match, Krul revealed he told Ozil that Arsenal were fortunate to have been given a second bit of the cherry. "But from what I heard it was quite obvious, that's what the results are for".
"It was a shame to concede a penalty like that".
"Yeah, it was a shame because obviously we were so solid all the game through and it was just a setpiece that killed us really with that".
Arsenal began brightly but the defensive frailties which have characterized their recent form showed themselves again as Norwich's Finnish striker Teemu Pukki scored his first goal since September.
Norwich remain second from bottom with 11 points from 14 games while Arsenal are eighth.