Frankfurt captain Alex Meier drilled in a low shot off the post after a quick passing move for his fifth goal of the campaign in the 57th minute but that was their last attacking move.
Substitute Marvin Ducksch's first touch of the ball was a thundering left-footed shot from the edge of the box that drew the hosts level and captain Uwe Huenemeier put them ahead in the 79th.
Another substitute, Stefan Kutschke, sealed their second away win of the campaign as the Bundesliga minnows, with a budget of just five million euros, moved to seventh on 12 points.
Frankfurt, who suffered their second loss of the season, dropped to eighth on goal difference.
Hamburg SV had to come from a goal down to draw 1-1 against Hoffenheim, extending their long run without a home win to more than six months.
Anthony Modeste gave the visitors the lead, slotting through keeper Jaroslav Drobny's legs in the 14th. Pierre-Michel Lasogga levelled 10 minutes before the break and hit the crossbar with a thundering drive in the 79th.
Hamburg also had Drobny to thank for the point after the 35-year-old former Czech international repeatedly denied Hoffenheim with a string of superb saves as Hamburg have now failed to win at home since April.
Leaders Bayern Munich crushed Werder Bremen 6-0 on Saturday to protect their four point lead with Borussia Moenchengladbach in second after beating Hanover 96 3-0.
(Reporting by Karolos Grohmann, editing by Pritha Sarkar)
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