Mustafi was a major doubt for the match after struggling to recover from a concussion.
Gibbs added to Arsenal's woes when he suffered a thigh injury this week.
With Laurent Koscielny suspended and Gabriel out injured with a knee problem, Mertesacker was in line to make his first start of the season.
But the club captain was not in the pictures released by the club and it means Arsenal boss Arsene Wenger could be without five first-team defenders at Wembley.
Arsenal v Chelsea combined XI Fri, May 26, 2017
Arsenal take on Chelsea in the FA Cup final – but would any of Arsene Wenger's players get into Antonio Conte's team?
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GK: Thibaut Courtois
The out-of-favour Mathieu Debuchy and Carl Jenkinson both joined in with the session
The out-of-favour Mathieu Debuchy and Carl Jenkinson both joined in with the session and could be forced to deputise in defence for Arsenal.
Debuchy's only appearance of the season came against Bournemouth in November 2016 and Jenkinson last played the EFL defeat to Southampton on November 2016.
Arsene Wenger oversees Arsenal training at London Colney
On Wednesday, Wenger bemoaned the loss of key players for such a big match.
“It just shows you how unpredictable football can be; it’s absolutely unbelievable,” said Wenger.
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“We have been hit hard in a position where we will need to be strong on Saturday.”