Dutch international Wout Weghorst headed home the winning goal with eight minutes remaining to lift his side to sixth and into the Europa League qualification spot, his 12th of the season.
By stark contrast, Florian Kohfeldt’s slumping side is second-from-bottom, six points from automatic safety and three adrift of the relegation playoff place, with just four games remaining.
Since the inception of the Bundesliga in 1963, Werder has been in the German top flight for 55 years, only being relegated in 1980 before bouncing straight back the following season.
But the double winners in the 2003/04 season have struggled in recent years and form has been poor since the restart of the current campaign, losing two straight home matches.
A visit to bottom side Paderborn next weekend and clash with relegation rivals Mainz could prove crucial, but Werder must also face Bayern Munich in a fortnight in a match that could see Bayern seal an eighth straight Bundesliga crown.
“The last two defeats at home have been very disappointing. We have to win next week. We’ll fight until the end,” Werder captain Niklas Moisander told the club’s social media feed.
Before kickoff, both teams gathered around the center circle at the Weser Stadium before dropping to one knee, repeating a gesture made by Borussia Dortmund and Hertha Berlin players on Saturday.
A later 1-1 home draw for Union Berlin against Schalke has hardly helped the Werder cause.
Union was heavy favorites to be relegated before the start of the season, but has pulled seven points clear of Werder with a precious draw in the capital.
Schalke, with just one point from 15 since the restart of Bundesliga action, trailed to Robert Andrich’s 11th-minute opener, but at least salvaged a point through a 28th minute strike from Jonjoe Kenny, who is on loan from English Premier League side Everton.
Echoing the pre-match proceedings at the earlier match, both teams also took to the knee in a gesture against racism first made by NFL player Colin Kaepernick in 2016.