Kevin de Bruyne gave the northern club the lead midway through the first half before Srdjan Lakic levelled for the Eagles.
But with Augsburg and Fortuna Dusseldorf both losing, the point was all Bremen needed to move four points clear of the relegation zone and ensure top-flight football will be played at the Weser Stadion again next season.
Frankfurt, meanwhile, still need a point on the final day of the season to qualify for the Europa League.
The home fans showed their support for Bremen like they had done a week ago, lifting Thomas Schaaf's men with their vociferous backing.
De Bruyne gave them something to cheer in the 22nd minute, when he showed why Borussia Dortmund and Bayer Leverkusen are fighting over the on-loan Chelsea midfielder's services next season by beating Oka Nikolov from just inside the penalty area.
The Belgian went close to a second in the 35th minute, but his shot was just wide of the post.
A minute later, he showed his defensive qualities to clear the ball ahead of Takashi Inui.
Frankfurt ended the half well, though, and came out with more determination in the second half with Lakic levelling in the 51st minute.
Karim Matmour burst through before pulling the ball back to Lakic, who just had to sweep the ball into an open goal.
Frankfurt increased the pressure with the Bremen fans getting nervous, with thoughts of the two late Hoffenheim goals last weekend certainly on most people's minds.
The news that Augsburg had fallen further behind against Bayern Munich did not settle them but the final whistle did, sparking scenes of celebration inside the Weser Stadion.