Haaland, who hasn't played since January 22 due to what the club says are muscular problems, was among 10,000 spectators permitted on Sunday under new nationwide coronavirus restrictions. Germany coach Hansi Flick was another.
Haaland, Dortmund's top goalscorer with 16 goals in 14 Bundesliga appearances this season, has been the subject of intense transfer speculation.
His team's latest performance will have done little to encourage him to stay as the defeat allowed Bayern Munich to pull nine points clear of Dortmund at the top of the table.
"A catastrophic day for us," Dortmund captain Marco Reus admitted.
"Consistency is the keyword," added beleaguered coach Marco Rose, whose team have endured repeated setbacks including a German Cup exit to second division St. Pauli last month.
In the 10th minute, Florian Wirtz pressured Dan-Axel Zagadou into playing the ball to Leverkusen's top scorer Patrik Schick, whose shot was saved by Gregor Kobel, only to rebound back in off the retreating Manuel Akanji.
Dortmund equalised through another own goal six minutes later, when Leverkusen defender Jeremie Frimpong got the final touch to Julian Brandt's free kick.
The 18-year-old Wirtz replied on a brilliant counterattack for Leverkusen four minutes later and Robert Andrich made it 3-1 in the 28th with a perfectly placed free kick inside the top left corner.
Jonathan Tah made it four in the 53rd with the next spectacular goal, firing a volley in under the bar after Dortmund failed to clear a corner and Moussa Diaby wrapped up the rout on another counterattack in the 87th.
Dortmund substitute Steffen Tigges capitalised on a rare lapse by Leverkusen to score in injury time, but it didn't prevent boos and whistles from the home team's fans.
In the day's other game, Wolfsburg ended their 11-game winless streak across all competitions with a 4-1 victory over last-place Greuther Furth.
Aster Vranckx scored twice, and Maximilian Arnold and Maximilian Philipp got the other goals, to lift Wolfsburg out of the relegation zone and jump up to 12th in the 18-team league, two points above Augsburg in the relegation play-off place.
