Aubameyang was named among the substitutes at the Emirates Stadium but was introduced after just 30 minutes following a serious injury suffered by Danny Welbeck .
Arsenal have officially qualified for the last-32 of the Europa League.
The Gunners were beaten 2-0 at home by champions Manchester City in their opening competitive game under the Spaniard before losing 3-2 at Chelsea in their second match.
Sokratis started the match- as the Islington Gazette revealed three hours before the game after speaking with a well-placed source.
"He was working well and he was having a good match", said Emery.
"This could be a break of something in the ankle", stated Emery.
England manager Gareth Southgate included Welbeck in his squad earlier in the day for an upcoming friendly against the United States and a Nations League tie against Croatia days later.
It was the hosts that took the game to their opponents, and they were lucky to still be on level terms before half-time.
Matteo Guendouzi is available once more after his one-match suspension, while Alex Iwobi and Henrikh Mkhitaryan will compete for a spot on the right flank.
Stephan Lichtsteiner played the ball into the 27-year-old in a crowded box.
The attacker required an oxygen mask as he was treated on the pitch, with a leg brace also in place after landing awkwardly on his ankle while trying to attack a header from his Swiss colleagues' centre.
Keown said: "He is the closest thing to Thierry Henry that I have seen since he left the club, he really is that good".
The Gunners won their first three group games, but were held to a 0-0 draw by Sporting Lisbon last night at the Emirates.
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