St Pauli captain Jackson Irvine was unable to play as he waits to come back from injury but his fellow Australia international Connor Metcalfe came on as a late sub as they prevailed on a big night at a packed Volksparkstadion.
Goals by Adam Dzwigała and Andreas Hountondji gave the visitors all three points in what was the first Bundesliga clash between the sides for 14 years.
The game, between clubs whose clash of styles and ethos have long marked the derby out as one of the world's most interesting, began to a raucous backdrop in front of 57,000 fans.
St Pauli took the lead after 19 minutes, when Polish centre back Dzwigała got on the end of Pereira Lage's cross and his shot was too strong for the outstretched hand of goalkeeper Heuer Fernandes.
Fans of the once mighty European champions Hamburg went crazy three minutes into the second half when Ransford Konigsdorffer appeared to score an equaliser but the goal was chalked off for offside.
Things got worse barely 10 minutes later, when Joel Fujita's defence-splitting pass put Andreas Hountondji through on goal and he rounded the keeper before converting from the tightest of angles.
There was no way back for the home side after Giorgi Gocholeishvili was sent off for a second bookable offence 13 minutes from time.
Midfielder Irvine has become a cult figure at St Pauli but has been out of action for club and country since undergoing foot surgery in April.
He did, however, participate in St Pauli's pre-season training camp and is reported to be close to making his return.
With AAP
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