Arsene Wenger appeared to confirm the Aubameyang deal had been completed following Arsenal's 3-1 defeat to Swansea on Tuesday in a video leaked online.
But, speaking to reporters after the game, Wenger declined to confirm he was confident the deal would go through and described the transfer as "complicated".
A £60m fee has been agreed with Borussia Dortmund for the 28-year-old striker, who arrived at Arsenal's London Colney training ground by private jet on Tuesday afternoon.
However, it is understood Borussia Dortmund would not sign off the transfer until they find a replacement.
Olivier Giroud, Michy Batshuayi and Anthony Modeste were among the names being considered by Dortmund, who are looking to secure a signing before the Bundesliga transfer window closes at 5pm on Wednesday.
Wenger admitted Giroud may have played his last game for Arsenal after coming on as a substitute in the defeat to Swansea.
Aubameyang did not testify as planned at Monday's trial hearing over the attack on the Dortmund team bus in April 2017 because of illness, and was booed by a section of Dortmund fans during last Saturday's 2-2 Bundesliga draw with Freiburg.
A banner in the crowd read: 'No player is bigger than our club'.