The France international, the subject of a failed bid from Barcelona earlier in the week, was suspended by Dortmund for skipping training and missed this clash, but it mattered little against their sixth-tier hosts as Aubameyang punished some woeful defending after Marc Bartra's opener.
One week out from the start of the Bundesliga season, Peter Bosz's men were predictably dominant - even if they laboured a little in the time between Bartra's effort and Aubameyang's 41st-minute penalty.
Aubameyang's second then arrived just as Rielasingen were starting to threaten on the break and allowed Dortmund to coast through the closing stages, with his hat-trick goal arriving 10 minutes from time to make him the club's most prolific foreign scorer.
Dembele had dazzled and scored in May's final triumph over Eintracht Frankfurt and, while his magic was not missed in Freiburg against last season's South Baden Cup winners, attention will now turn towards an announcement from the club, expected on Sunday, regarding the winger's future.
A packed Rielasingen defence kept their esteemed visitors at bay early on, but the opener arrived after 12 minutes as Bartra met Jan-Niklas Beste's cross to stab a finish under Dennis Klose.
Dortmund had capitalised on the home side's failure to reorganise after a half-cleared corner and, although Danny Berger drew a save from Roman Burki at the other end in a rare forward foray, another defensive error teed up a second.
Maximilian Philipp ran clear and then went down under Klose's challenge as he rounded the goalkeeper, with Aubameyang coolly dispatching the subsequent penalty beyond Rielasingen's cautioned captain.
The goal was just reward for Dortmund's dominance and Mahmoud Dahoud dragged wide as the visitors chased a third before the break.
An offside flag correctly ruled against Andre Schurrle as he volleyed into the net shortly after the restart and Aubameyang then tested Klose with a header towards the bottom-right corner.
Rielasingen refused to give up hope of forging a route back into the tie, but a series of counters brought only routine stops from Burki and Dortmund soon put the result beyond doubt.
After 55 minutes, Aubameyang, who had tamely shot straight at Klose moments earlier, took the ball on halfway and sprinted through on goal to lift a left-footed finish over the keeper.
Philipp then lashed wide from a good position inside the area and Sebastian Stark was similarly wasteful for the home side, before Nuri Sahin's stunning strike from distance clipped the outside of the post.
But it was Aubameyang who had the final say, brushing an off-balance defender aside in the area to guide the ball into the net and Dortmund into the next round.