VfL Wolfsburg, under new coach Steve McClaren, had to wait until the 80th minute to break the resistance of regional league club Preussen Muenster, with Brazilian Grafite scoring the winner two minutes from time in their nervous 2-1 win.
So far all but two top-flight clubs - St Pauli and Hanover 96 - have survived the tricky one-leg first round ties, with title holders Bayern Munich and Schalke 04 in action on Monday.
Amateurs Torgelower stood their ground early on against Hamburg and keeper Andre Greulich was kept busy, denying Mladen Petric after 13 minutes.
Greulich was beaten though in the 34th minute when Van Nistelrooy scored from close range after Jonathan Pitroipa had hit the post from close range.
The hosts came back and two minutes before the break netted an equaliser with a nice solo effort from Daniel Pankau.
Their joy was short-lived, however, with Peruvian striker Paolo Guerrero firing in an 18-metre free-kick to put Hamburg back into the lead eight minutes after the break.
Van Nistelrooy added two more midway through the second half and David Jarolim rounded off the scoring nine minutes from time.
Wolfsburg struggled against amateurs Muenster, with Bosnian striker Edin Dzeko missing several clear scoring chances early on.
Dzeko, who is reported to be wanting to leave the 2009 champions, did make the score sheet, albeit with one own goal.
Last season's top scorer first did well to set up Cicero for the lead in the 80th minute but six minutes later failed to clear a free-kick, deflecting the ball into his own goal.
Grafite, the 2009 Bundesliga top scorer, came to the rescue only two minutes later, and, set up by a Dzeko header, scored the winner to rescue former England coach McClaren from a major embarrassment in his first competitive match in charge.
Earlier on Sunday, Mainz, without striker Aristide Bance, who hours earlier had agreed to join Dubai-based Al Ahli, edged past Berliner AK 2-1 while Nuremberg beat Eintracht Trier 2-0.
