Gabriel Martinelli will undergo a scan on an injured ankle, according to Arsenal boss Mikel Arteta.
Martinelli had been named in the starting eleven for Saturday evening's game but had to be replaced by fellow youngster Reiss Nelson after suffering an injury in the warm-up.
Martinelli returned to action in December after a prolonged absence due to a knee problem but is now set for another spell on the sidelines.
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"I am gutted. I was in my office before the game and one of the coaches came in and told me that Gabi had hurt himself, that he'd twisted his ankle," Arteta told press after the game.
"I went to the medical room and he was in tears. He was in a lot of pain and we're going to have to see how he is. It didn't look good. I imagine that we're not going to have good news with him.
"We really want to know what's going on. He's a character and he wants to play. He doesn't care and can handle pain but I don't know. Hopefully there is nothing too serious but to start with, it didn't look too good."
Emile Smith-Rowe and Pierre-Emerick Aubameyang both scored in extra time to to secure a fourth consecutive win for the team and qualify for the FA Cup fourth round.
Arsenal, who are 11th in the Premier League with 23 points from 17 games, host 14th placed Crystal Palace on Thursday.
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