The Gunners were unable to maintain an unbeaten run in the competition, but had already qualified for the knockout stage of the Champions League before going down 3-1
The defender sprained his ankle as his side went down in Greece, but the result mattered not as the Gunners still finished top of Group F having already qualified.
“Santos suffered a bad ankle injury. It looks like he will be out for a while. We have [Kieran] Gibbs coming back in two to three weeks," he told reporters.
“Hopefully Santos will not be too long but, for Saturday against Everton, he looks to be struggling."
The Frenchman fielded a side made up of youth and fringe players and this move came undone as a handful of defensive mishaps handed victory to the hosts, who missed out on qualification thanks to Marseille's late win at Dortmund.