Frankfurt were the better team for periods of the game but Felix Wiedwald played his part to ensure they kept just their second clean sheet of the season.
However, Papy Djilobodji turned out to be their unlikely hero with an 88th minute winner.
Drab first half
Eintracht almost got off to the perfect start against their relegation rivals, only for a superb save from Wiedwald to keep out Änis Ben-Hatira's powerful, glancing header down low to his left. Bremen had an opportunity of their own - in what was a lively opening five minutes - but Claudio Pizarro couldn't make contact with a dangerous cross.
Werder were struggling to get any sporting of attacking move together, in what was proving to be a half of few chances. Instead of testing Lukas Hradecky, the hosts were only putting more pressure on Wiedwald, who made a solid stop to keep out Makoto Hasebe's drive and divert it wide.
Bremen's onl real threat to the Frankfurt goal came from set-pieces in the first period, though even that was a hit and hope exercise. No-one was able to win the first ball, or the second, and even when it did drop for the hosts any efforts was bravely blocked by a defender. All in all, a forgetable half.
Delight for Djilobodji
The first 15 minutes of the second 45 brought little change from either side, even though Bremen did seem to have moved into a slightly more attacking style. Several crosses were fired into the box but really proved dangerous for Hradecky and his defence; in fact, Frankfurt were confident in dealing with the aerial bombardment.
As the half wore on, tempers flared and tensions raised. The chances also seemed to come to the fore, something that had been lacking all game, as Zlatko Junuzovic slipped at the vital moment to scuff wide before Anthony Ujah was halted by Hradecky at his near post.
However, as the cards racked up, Werder ramped up the pressure and were rewarded right at the very end. A hopeful ball into the box was throw in by Junuzovic and met by Ujah, who managed to find Djilobodji. The defender somehow scrambled the ball in from the by-line. Cue beer, shirts and people being thrown up in the air at the Weserstadion; Frankfurt, however, will have to try and save themselves in the relegation play-off.