The Chilean, linked with a move away from north London, is yet to return to training after suffering illness and is not expected to return to training at London Colney until July 30.
Mustafi will also miss clashes against Benfica and Sevilla. 'Alexis and Mustafi, their first training session will be on Sunday, the day we play against Sevilla [in the Emirates Cup]', Wenger told Arsenal's official website.
Jack Wilshere, on the other hand, is deemed surplus to requirements and, after missing the Gunners' tour of Australia and China, has also been left out of the squad for the Emirates Cup.