Zlatko Junuzovic decided matters in the 19th minute of a game which started with Bremen in dominating form, saw Hamburg recover for the start of the second half only to end with Bremen again in the ascendency.
The result puts six points between the two sides with Hamburg stuck inside the bottom three in Mirko Slomka's second game in charge.
The match started with Bremen urged on by their fans, and responding well.
Nils Petersen and Franco Di Santo both had early opportunities to give Robin Dutt's men the lead as Hamburg, who had beaten Borussia Dortmund 3-0 a week ago to end a run of five successive defeats in all competitions, did not know what hit them.
The home side's pressure paid off in the 19th minute when Junuzovic popped up in front of goal and slotted the ball under Rene Adler from close range as the Hamburg defence was caught napping.
Junuzovic also hit the post as Bremen looked for a second, although Raphael Wolf had to turn a Hakan Calhanoglu effort onto the crossbar to keep them ahead at the interval.
Hamburg transformed at the start of the second half with Rafael van der Vaart on for Tomas Rincon as smoke from flares forced a short break in the play.
When the game restarted, it was Slomka's men who looked more likely to score and Wolf was much busier keeping shots out from Milan Badelj.
Werder regrouped and regained the initiative with Petr Jiracek doing well to keep a Santiago Garcia effort out after Adler pushed Ludovic Obraniak's header over the bar.
Now warranting their lead again, Bremen took no more risks as they survived even six minutes of stoppage time to take the spoils.