The game in front of 57,000 fans in Hamburg's Volksparkstadion started 15 minutes late due to heavy traffic and long queues for increased security checks following the attacks that left 130 dead and hundreds injured in the French capital last week.
The win lifted Hamburg, who needed a relegation playoff to stay up last season, to seventh on six points.
Bayern Munich's Robert Lewandowski and Arjen Robben scored twice each as the champions crushed Hanover 96 4-0 in the Bundesliga on Saturday to go four points clear at the top of the table as rivals Borussia Dortmund lost to Hamburg SV.
Schalke 04 striker Klaas-Jan Huntelaar could not have dreamt of a better comeback after five months out when he scored the opening goal in his side's 3-0 victory at Hamburg SV on Sunday.
Holders Bayern Munich eased into the German Cup third round with a comfortable 3-1 win at Hamburg SV on Wednesday to continue their unbeaten domestic run as they prepare for Saturday's league clash against Borussia Dortmund.
Borussia Dortmund steam-rollered hapless Freiburg 5-0 while Bayern Munich plodded past VfL Wolfsburg 1-0 as the two unbeaten arch-rivals remained level on points at the top of the Bundesliga on Saturday.