Ante Rebic put Eintracht ahead in the 17th minute when he curled home a fine finish for his fourth goal in his last six games.
However Bremen, under the guidance of the club's under-23 coach Florian Kohfeldt after the sacking of Alexander Nouri earlier in the week, levelled soon after through Niklas Moisander's maiden Bundesliga goal.
That was also Bremen's first league goal in 508 minutes but it was not enough to save them from defeat as in-form Frenchman Haller struck a deserved winner for Frankfurt in the 89th minute.
The result lifts Eintracht into the top five ahead of the weekend fixtures, with Bremen still stuck in the bottom two without a victory from 11 games.
