Returning from their flawless tour of America, the Gunners were brought back down to earth by their fellow Premier League side.
Bryan Muembo scored for the Bees after just nine minutes, set up by a great pass from Ryan Trevitt.
Eddie Nketiah equalised for the Gunners with his fifth goal of preseason after some neat link-up play between Reiss Nelson and Ainsley Maitland-Niles.
Mikel Arteta's side dominated the second-half but it was the visitors who got themselves ahead.
This time it took a bursting from Rico Henry to split open the Arsenal defence, and his cross eventually found Trevitt, who finished calmly past Matt Turner.
Arsenal: Turner, Cedric, Walters (Awe 46), Holding, Tavares (Souza 76), Elneny, Lokonga, Maitland-Niles (Patino 85), Marquinhos, Nelson (Sagoe Jr 90), Nketiah.
Brentford: Strakosha (Cox 62), Stevens, Bech, Crama, Henry (Racic 62), Onyeka, Ghoddos (Yarmolyuk 75), Peart-Harris, Trevitt, Lewis-Potter, Mbeumo (Gilbert 75).
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