Aubameyang endured a forgettable outing as Dortmund went down 1-0 in Lisbon in the opening leg of their last-16 tie.
The 27-year-old forward, who leads the Bundesliga with 17 goals, missed a second-half penalty and spurned two excellent chances before he was substituted in the 62nd minute on a dismal night at Estadio da Luz.
And Dortmund head coach Tuchel explained Aubameyang's early withdrawal as the German visitors attempted to cancel out Kostas Mitroglou's opener.
"Aubameyang is not fully fit after the African Nations Cup," Tuchel said via UEFA.com. "His body language did not suggest that he would do better after giving away the penalty."
Dortmund enjoyed the better chances but Benfica made the most of their opportunities on home soil.
Mitroglou's opportunistic strike settled the opening leg, the Greece international converting following a header from team-mate Luisao.
However, Tuchel could not fault his players despite the loss in Portugal.
"It is an extremely complicated result, but I am very proud of how we played tonight. Even though I am very disappointed, I am proud of how we presented ourselves," he added.
"I don't think we played well, I think we played outstandingly. That's only possible in football, to play this well and to still lose. Luckily, there's a return leg for such games.
"They attacked us differently after the break, we were not prepared for how they attacked our back three. Had we played two long balls in those situations, nothing would have happened."