He was later seen limping out of the Allianz Arena, though was walking unaided and without crutches.
"He's got another MRI this afternoon because he had quite a lot of fluid in the area so it was difficult to understand the extent of the injury,” Arteta said of Saka at his pre-Everton press conference on Friday. “We will know more tomorrow.
"We need a few more scans and opinions from the specialists. When a player is struggling to walk without any pain, he's restricted in movement, they are not good signs. Let's be a little bit patient so we can gave a definitive assessment."
Major blow: Bukayo Saka was injured playing for Arsenal against Bayern Munich in the Champions League
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Saka's absence is a major blow for Arsenal. Since the 2020/21 season, the Gunners have a win rate of 64.2 per cent in the Premier League when he plays compared to 53.3 per cent when he does not.
Arteta is also already short of wingers. Christos Tzolis remains out and Arsenal sold both Gabriel Martinelli and Leandro Trossard in the summer.
Noni Madueke and Eberechi Eze are set to be relied upon in the coming weeks, while there should also be opportunities for Max Dowman.
In more positive news for Arsenal, Piero Hincapie will return from an ankle injury to face Everton on Saturday.
The defender has missed the last three matches after picking up the issue on the Emirates Stadium pitch during a training session held immediately after the win over Leeds last month.
Hincapie returned to the grass earlier this week and went through some individual training drills on Tuesday. He trained again on Friday and will be available this weekend.
“He trained with us and is available for tomorrow,” Arteta confirmed.
The game will come too soon for Tzolis in his recovery from a hamstring injury suffered while playing for Greece earlier this month, but he is understood to be close to a return.
William Saliba is also making good progress in his recovery from a serious back injury sustained at the World Cup that has prevented him from playing at all so far this season, but he is not in contention to feature yet.