The Gabon international, who has scored 21 goals in 23 appearances thus far this season, has been heavily linked with a move away this month.
After Dortmund were forced to deny reports that a deal had been agreed over a summer switch to a Chinese club, Arsenal soon emerged as the frontrunners to sign him, with Arsene Wenger keen to compensate for the impending loss of Alexis Sanchez.
With the Chilean set to join Manchester United, Arsenal are looking to invest heavily and Goal understands they have agreed personal terms with Aubameyang and Manchester United's Henrikh Mkhitaryan.
Watzke has now confirmed that a formal offer has been lodged by the Premier League club, with reports suggesting that Dortmund value Aubameyang at £53 million.
"I can confirm that there has been a first request from Arsenal for Pierre-Emerick Aubameyang and we are not commenting on the sums that have been called from England since noon today," he said, per Ruhr Nachrichten.
Watzke’s admission comes just a day after BVB transfer chief Michael Zorc dismissed talk of a deal with the London club as "rubbish", having already hit out at Wenger for being 'disrespectful' in suggesting negotiations were going on.
However, Dortmund have also been heavily critical of Aubameyang over his conduct recently. He has been the subject of several controversial moments this season and has been dropped twice in recent months for disciplinary reasons.
The forward was left out of last week’s draw against Wolfsburg after missing a team meeting and was warned by Zorc that his behaviour cannot continue.
"I don't know what's going on inside his head," he said. "We had a very contentious discussion today. We're not used to this behaviour from him. It can't go on like this."
Having joined Dortmund in 2013, the 28-year-old's goal record at Signal Iduna Park is exemplary, scoring 141 times in just 212 appearances, while his contract runs until 2021.
Dortmund have struggled this season, though, and currently sit third in the Bundesliga, 14 points behind leaders Bayern Munich. Arsenal, meanwhile, sit sixth in the Premier League, 23 points behind leaders Manchester City.