Last season's beaten finalists are due at Emirates Stadium on Tuesday for a potentially crucial showdown in Group F.
The Gunners lead the way at present, having collected maximum points from their two games so far.
Dortmund responded to a shock reversal against Napoli on Matchday One with a convincing 3-0 win over Marseille, but laboured to a 1-0 Bundesliga victory against Hannover on Saturday and Aubameyang admits a marked improvement will be required in north London.
The Gabon international, who has netted five goals since joining from St Etienne over the summer, said: "Playing Arsenal won't be easy at all and we'll have to do much better than we did on Saturday.
"We didn't have our usual rhythm and didn't play the high-tempo football we normally do.
"Some of our players have only just returned from injuries and we haven't been able to train properly.
"I had the impression some of us were already tired going into the game, and it got worse as the match progressed."
Aubameyang acknowledges that Dortmund cannot afford to put in another lethargic display in midweek, with Arsenal boasting a number of players on top of their game right now.
He added: "(Mesut) Ozil is in great form and is crucial to Arsenal's game, but they're a quality side anyway.
"Olivier Giroud, for example, is also a very good player. I know him well from my time in France, he's a dangerous striker."