A second-half Nils Petersen goal was enough to earn the German outfit revenge for their 2010 friendly defeat, with the Cottagers unable to carve out many chances
Martin Jol's side struggled to carve out chances throughout and slumped to their first defeat in pre-season after allowing the striker to grab his third goal in just two games.
Dutch winger Eljero Elia could have in fact put the home side ahead after just 15 minutes but headed a Clemens Fritz cross wide from close range before Fulham were dealt a blow when Alexander Kacaniklic was forced off with an injury.
The Swede went down following a challenge on the left-hand side and, after receiving treatment, was replaced by Na Bangna as the visitors played it safe.
After that short break had disrupted play, there were few other talking points prior to the end of the first half barring Fritz's narrow miss following a mazy run.
However, it took just seven minutes of the second half for a goal to come, when Petersen coolly rounded Maarten Stekelenburg and finished well.
Elia almost made it two shortly after but put the ball wide after Stekelenburg parried an Aaron Hunt effort.
A raft of substitutions largely disrupted the game's flow after the hour mark, meaning that Bremen did not struggle see out a win which avenged their 5-1 friendly defeat to Fulham in August 2010.