The Brazilian centre-back collided with Kelechi Iheanacho in stoppage time as both players battled for a loose ball which left Gabriel needing more than six minutes of treatment on the leg injury he picked up before leaving the field.
Both teams named strong line-ups for the friendly and the quality was on show as Alex Oxlade-Chamberlain and Francis Coquelin wasted great efforts to break the deadlock.
But it was Pep Guardiola’s side that took the lead after 30 minutes when Sergio Aguero converted Raheem Sterling’s right-wing cross.
Alex Iwobi curled in an equaliser on 50 minutes before Theo Walcott put the Gunners in front with a deft chip over Joe Hart after being played through by Alexis Sanchez.
Chuba Akpom capitalised on sloppy City defending to extend Arsenal’s lead before Iheanacho headed a consolation goal from Jesus Navas’ cross.
Jurgen Klopp got a rude awakening on his return to former club Mainz as the German side romped to a 4-0 victory over Liverpool.
The Reds won by the same scoreline against Barcelona at Wembley the day before but it was a much-changed side that fell to the club where Klopp started his managerial career.
Alex Manninger, a summer signing from Mainz, started in goal for the visitors but could not stop Daniel Brosinski and Jhon Cordoba putting the home side two up at the break.
Yunus Malli and Yoshinori Muto also got on the scoresheet to condemn Liverpool to defeat in their last match before their Premier League opener at Arsenal on Sunday.
Chelsea’s final preparations before the new season ended with a 4-2 win at Werder Bremen.
Eden Hazard, Oscar and Diego Costa netted one apiece in the first half, which also saw former striker Claudio Pizarro score from the penalty spot for Bremen. Lennart Thy pulled another goal back for the hosts before Pedro sealed the victory in stoppage time.