The meeting, which took place in Bremen, ended with a score of 2: 1 in favor of the guests.
Borussia's victory was brought by goals from Rafael Guerreiro, who scored in the 12th minute, and Marco Reus, who scored in the 78th minute.
Werder Bremen responded with a goal from Kevin Möwald, who scored in the 28th minute.
Borussia, gaining 22 points, is ranked fourth in the Bundesliga standings.
Werder Bremen with 11 points - 13th.
Earlier, Borussia Dortmund announced the resignation of Lucien Favre.