Goals by Greek striker Angelos Charisteas and midfielder Holger Wehlage were enough to give Bremen the points as Hamburg could only reply through Czech defender Tomas Ujfalusi's header from a first half corner kick.
The win takes Bremen to ninth in the German league table, while Hamburg remain in sixth position after two matches.
In the other Sunday Bundesliga match, Wolfsburg moved to seventh with a 1-0 victory against Borussia Monchengladbach at the VfL-Stadion.
Striker Martin Petrov scored the winner just after the hour mark to give Wolfsburg their first league victory of the new season.
Gladbach remain well down Die Bundesliga table in fourteenth, having yet to register a victory after a draw and a defeat in their first two league matches.
Click below for match stats:
Bundesliga
Werder Bremen 2-1 Hamburg
Wolfsburg 1-0 Borussia Monchengladbach
Click here for an updated Bundesliga table.
