Jurgen Klopp's men needed until the 73rd minute to break the deadlock against the Italian opposition, with the Gabon international on hand to score from close range
The Colombia striker - who linked up with Dortmund after agreeing to join from Bundesliga rivals Hertha Berlin in April - played the first half in Austria, in a largely lacklustre encounter which was settled by the in-form Aubameyang.
After a 5-1 win over Rot-Weiss Essen last Sunday, Serie A side Chievo represented a step up in class for Dortmund.
The Verona outfit proved to be tough for Dortmund to break down and appeared set to hold on for a valiant draw until Gabon striker Aubameyang popped up in the 73rd minute to earn victory for the German side, the substitute netting his fourth goal in five pre-season games.
The first half was largely bereft of chances and surprisingly lacking in entertainment considering that Dortmund had scored 14 goals in their previous four friendlies.
Jurgen Klopp's men were able to have more of the ball in the second half, but clear sights at goal were few and far between.
However, just when Chievo looked set to hold firm Aubameyang, brought on for Ciro Immobile at half-time, struck from close range.
The former Saint-Etienne talisman slotted home at the far post after Ramos' replacement, Ji Dong-Won, had flicked a corner into his path.
Dortmund take on Slask Wroclaw, Athletic Bilbao and Liverpool in friendlies before their first competitive game against Bayern Munich in the DFL-Supercup on August 13.