Reus' return after six weeks out was a welcome boost for a side still struggling to deal with Tuesday's bomb attack on the team bus in Dortmund in which defender Marc Bartra was wounded.
''It was a great performance of character that cannot be rated highly enough from my side,'' coach Thomas Tuchel said as Dortmund consolidated fourth place amid increased security.
''Gol!!!!!'' said Bartra on Twitter. The Spanish defender, who had an operation on his hand and arm, was able to watch the game at home following his release earlier after four nights in the hospital.
Marco Fabian equalized inside the half-hour mark with a brilliant strike in off the top of the post from 25 meters (yards), but Sokratis Papastathopoulos restored the home side's lead in spectacular fashion a little more than five minutes later.
Sokratis, a defender, wrong-footed one of his counterparts with a dummy and let fly inside the far post.
Reus, who was busy throughout the first half, was taken off at the break with a view to the second leg of the Champions League quarterfinal in Monaco next Wednesday.
''Just a precaution,'' said Dortmund, which lost the postponed first leg 3-2 one day after the bomb blasts.
Ousmane Dembele, who came on for Reus, set up Aubameyang to seal it late on a counterattack. It took Aubameyang's tally to a league-leading 26 goals, level with Bayern Munich's Robert Lewandowski.
Afterward, Dortmund players held up a Bartra jersey in front of the Westfalenstadion's south stand, where fans chanted his name.
''An emotional moment,'' Tuchel said.
Bayern was playing later at Bayer Leverkusen.
LEIPZIG 4, FREIBURG 0
Yussuf Poulsen scored one and set up Timo Werner in the first half, before Naby Keita and Diego Demme made sure in the second as Leipzig kept its charge toward the Champions League going.
It was the promoted side's 19th win from 29 games, keeping it second, seven points behind Bayern ahead of the late game.
HOFFENHEIM 5, BORUSSIA MOENCHENGLADBACH 3
Hoffenheim is enjoying its best season in the top flight and Adam Szalai had the home side celebrating early with two goals before Jannik Vestergaard pulled one back and Lars Stindl equalized.
Kerem Demirbay restored the home side's lead and Mark Uth added another before Mahmoud Dahoud kept 'Gladbach in the game.
But Dembiray's second goal in the last minute killed any hopes of a comeback and kept Hoffenheim third, on course for automatic Champions League qualification.
WOLFSBURG 3, INGOLSTADT 0
An own-goal from Markus Suttner before the break and goals from Yunus Malli and Mario Gomez in the second half ended Ingolstadt's three-game winning run and left it in the relegation zone.
Wolfsburg, which was in danger of being overtaken by the visiting side, stayed one point above the relegation zone due to Augsburg and Mainz both winning.
Winless in six games, Augsburg got off to a great start with goals from Martin Hinteregger and Paul Verhaegh to beat Cologne 2-1.
Augsburg, which finished with nine players after late cards for Koo Ja-cheol and Alfred Finnbogason, remained in the relegation playoff place, four points above Ingolstadt and level with Mainz, which has a superior goal difference,
Danny Latza's deflected shot before the break was enough for Mainz to end its five-game losing streak with a 1-0 defeat of Hertha Berlin, which has now lost eight games in a row away from home.