A goalless draw with Cameroon put the Panthers out at the first hurdle, after they had played out 1-1 ties with Guinea-Bissau and Burkina Faso.
Aubameyang scored each of his country's goals in the tournament but a costly miss from point-blank range could come back to haunt the Borussia Dortmund man.
Jose Antonio Camacho was only hired as Gabon's coach in December after Jorge Costa was fired and the transition under the Spaniard led to the late starting of a pre-tournament training camp.
"It is really annoying because we had chances. Sadly there are days when it doesn't go in, like my first chance from two metres out," Aubameyang said. "We are all really disappointed. We didn't really have the time to prepare. We started a little bit late.
"But I am really proud of all the players, because everyone gave their all.
"I think we were stronger than every other team in the group, but it is about everything, the preparation, the change of coach, it wasn't easy."
Aubameyang was furious at the final whistle, walking straight off the pitch without shaking hands with any of Cameroon's players.
"Of course everyone is disappointed, it is usual in these situations," Aubameyang said. "The players feel it the most."