Dutch international Wout Weghorst took home the winning goal with eight minutes remaining to take his team to sixth place and reach the qualifying point in the Europa League, his 12th of the season.
In stark contrast, Florian Kohfeldt’s side in crisis is second from bottom, six points from automatic safety and three drifting from the relegation playoff spot, with only four games remaining.
Since the beginning of the Bundesliga in 1963, Werder has been in the German top flight for 55 years, only demoted in 1980 before bouncing back in the following season.
But the double winners in the 2003/04 season have struggled in recent years and the form has been poor since the campaign has restarted, losing two consecutive home games.
A visit to the lower part of Paderborn next weekend and a clash with relegation rivals Mainz could prove crucial, but Werder will also face Bayern Munich in two weeks in a game that could see Bayern sign an eighth consecutive crown in Bundesliga.
“The last two home defeats have been very disappointing. We have to win next week. We will fight to the end,” captain Werder Niklas Moisander told the club’s social media feed.
Before kick-off, both teams gathered around the center circle at the Weser stadium before falling on one knee, repeating a gesture made by players from Borussia Dortmund and Hertha Berlin on Saturday.
A subsequent 1-1 draw for Union Berlin against Schalke certainly did not help the Werder case.
The Union was a heavy favorite to relegate before the start of the season, but snatched seven points ahead of Werder with a valuable draw in the capital.
The Schalke, with only one point out of 15 since the restart of the Bundesliga action, moved on to the opening of the 11th minute of Robert Andrich, but at least he recovered a point in a 28-minute strike by Jonjoe Kenny, who is in loan from the English Premier League team Everton.
Echoing the pre-match proceedings of the previous game, both teams also took to their knees a gesture against racism made for the first time by NFL player Colin Kaepernick in 2016.