Former Gunners skipper Xhaka collided with team-mate Matteo Guendouzi and was replaced by Dani Ceballos after just eight minutes having seemingly injured his right ankle.
Mari, an ex-City defender on loan at Arsenal from Flamengo, appeared to pull his calf when chasing Kyle Walker, with experienced centre-back David Luiz entering the fray.
The quick substitutions could bring the issue of player fitness back to the fore following the three-month enforced break for the coronavirus pandemic.
City manager Pep Guardiola, who had an injury concern of his own when Riyad Mahrez appeared to be hobbling, said pre-game his team were not prepared for the flurry of 10 Premier League fixtures in the space of six weeks.
It was a positive test from Arsenal boss Mikel Arteta - Guardiola's former assistant at the Etihad Stadium - that decisively moved the Premier League towards suspension in March.