Dortmund coach Thomas Tuchel hauled the Gabon forward off after 62 minutes of his side's 1-0 defeat in Lisbon, during which he squandered two clear opportunities to score and hit a tame penalty straight at Benfica goalkeeper Ederson.
Tuchel insisted the 27-year-old had no problem with being substituted, and Aubameyang has reflected on growing fatigue.
Aubameyang was part of a Gabon side that crashed out of AFCON after three games despite being the host nation, and the tournament has taken its toll on him.
"I missed the preparation [for the second half of the season] through the Africa Cup of Nations," he told Bild.
"I have to admit, I'm a bit tired."