The Gunners captain leaped for a header with Gary Cahill in the first half of the match at Wembley Stadium and was caught in the face with an elbow.
The German suffered a nasty gash to his head and dropped to the ground in a heap with blood pouring from his face as the rest of his team looked on anxiously.
He received treatment from Arsenal’s medical team but was forced to make way.
Mertesacker was replaced by Arsenal new boy Sead Kolasinac, who has impressed for the Gunners on their pre-season tour of Asia.
And the introduction of the Bosnian left-back proved crucial for Arsenal after they fell behind following a Victor Moses strike moments after the break.
Arsenal were given a glimmer of hope in the last ten minutes of the game, which Chelsea looked to be seeing out comfortably.
Pedro was dismissed for a reckless challenge on Mohamed Elneny before Kolasinac made the Gunners’ numerical advantage count.
Sensing Chelsea were backing off, the Bosnian pushed forward to grab an equaliser and take the game to penalties.
Olivier Giroud then won the match for Arsenal with a decisive spot-kick after Thibaut Courtois and Alvaro Morata missed their penalties.