The news will come as relief to Arsenal fans, who were alerted by the interest of their Premier League rivals.
Aubameyang, 30, is out of contract in 2021 and an extension has not yet been offered.
The Blues were interested, but ESPN says the imminent arrival of RB Leipzig star Werner has ended their search for a striker.
The Gunners must now work hard to negotiate a contract with the Gabon international, who has simply been a goal machine for the club since arriving in 2018.
Given football's uncertain economic climate, Mikel Arteta will be hard tasked to find a replacement for a man who has scored 61 goals in 97 appearances for the club.