Hosts Dortmund hammered the visitors defence as Reus and Aubameyang contributed half of their side's 31 shots on goal, compared to Schalke's meagre three chances.
It was Dortmund's biggest derby win since 1998.
Borussia got the breakthrough when Aubameyang -- who had compared winning the derby to 'an orgasm' -- pounced on a mistake in the visitors' defence to roll the ball home on 78 minutes.
The 25-year-old celebrated by donning a 'Batman' hat, playing up to his 'caped crusader' nickname, with Reus wearing a 'Robin' mask as his side-kick.
Henrikh Mkhitaryan made it 2-0 when he netted 108 seconds after Aubameyang before Reus robbed Schalke goalkeeper Timon Wellenreuther to claim their third on 86 minutes.
"If you didn't know who Batman and Robin before, you do now," joked Aubameyang.
It emerged Aubameyang's translator Massimo Mariotti had hidden the costumes behind the Schalke goal.
Reus looked slightly sheepish when asked who had the idea.
"In the first half of the season we didn't have so much fun and we came up with it a few days ago while we were eating together," said the Germany winger.
"That was the game of the year, you can't have a better feeling during the season."
The victory lifts Dortmund to tenth in the table after picking up their fourth consecutive league win having started February bottom of the table.
A big part of Dortmund's revival has been down to both Aubameyang, who has scored five goals in his last four league games, and Reus' prowess in front of goal.
Dortmund-born Reus has scored in all five matches, including the 2-1 Champions League defeat at Juventus on Tuesday, since announcing he has extended his Borussia contract until 2019.
But he balked when asked about Dortmund's challenge for a European place as they now find themselves eight points from a Champions League place for next season.
"Four weeks ago we were standing here talking about the relegation battle," said Reus.
"We'll take this one game at a time, at the moment things look good but we have tough games ahead and there is still a long way to go."
Delighted Dortmund coach Jurgen Klopp singled out attacking midfielder Mkhitaryan for praise.
"That was a fantastic afternoon for us. We worked hard for a deserved result," said Klopp.
"The best celebration was for Mkhitaryan.
"Everyone wanted to jump on top of him when he scored, he had an unbelievable game.
"That was the best game he has played so far for Borussia Dortmund."
But Klopp was keen to point out that his team is still only five points from the relegation battle despite their up-turn in fortunes.
"We're only five points away, nothing has really changed," said Klopp.
"But we are on a good path and we'll continue on it."
Schalke coach Roberto Di Matteo apologised for his side's poor performance.
"It is a very difficult day for all of us," said the ex-Chelsea boss after losing his first derby since taking charge in October.
"We want to apologise to our fans for a poor display, we had planned things differently.
"We did well for the first 10 minutes, then we couldn't get the game under control."