Hosts Magdeburg, who in their heyday won three East German league titles and the European Cup Winners' Cup in 1974, held out for 41 minutes before Gonzalo Castro gave Dortmund the lead, one minute after coming on as a substitute.
Alexander Isek, Andriy Yarmolenko, with a penalty, Marc Bartra and Shinji Kagawa added further goals as the visitors ran riot in the second half.
Schalke 04 forward Franco Di Santo scored his first competitive goal for more than 18 months to set his side on the way to a 3-1 win at third tier Wehen Wiesbaden.
The former Wigan Athletic and Werder Bremen forward, who has suffered injury problems since his last goal against FC Cologne in March 2016, netted from close range after 27 minutes.
Guido Burgstaller added a second three minutes later before Alf Mintzel put through his own goal in the 54th. David Blacha scored Wiesbaden's consolation late in the game.
Eintracht Frankfurt won 4-0 at fourth tier FC Schweinfurt with Sebastian Haller scoring the first two goals.
Bayer Leverkusen thumped second tier Union Berlin 4-1, while a second-half Thorgan Hazard goal gave Borussia Moenchengladbach a 1-0 win at second division leaders Fortuna Duesseldorf.
(Writing by Brian Homewood; Editing by Ken Ferris)
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