In danger of slipping into the bottom three for the first time this season, Koln started quickly, with Michael Zetterer having to deal with Jakub Kamiński’s initial shot and Ragnar Ache’s prod on the rebound.
But the hosts had been imperious in Albert Riera’s first three home games in charge, and they soon started to dominate.
Their first clear chance came when Hugo Larsson played in Ansgar Knauff over the top, but his poke towards the far post was turned wide brilliantly by Marvin Schwabe.
Said El Mala then showed what he was capable of by finding space to curl just wide at the other end, while Schwäbe was again in fantastic form to deny Arnaud Kalimuendo one-on-one.
Most of the traffic remained in Koln's half from there, but arguably the best chance of the opening 45 minutes came on the break for the visitors.
El Mala raced through in a two-on-one situation, choosing to square it to Kamiński, whose first touch was too heavy to evade the onrushing Zetterer.
Both sides seemed desperate for the opener in a chaotic start to the second half, and the floodgates finally opened on 66 minutes.
Fares Chaibi broke through on the right for Frankfurt and pulled it back across for Jonathan Burkardt to pass into the open net, giving his side the confidence to push for a second.
They only had to wait a few minutes for Kalimuendo to pounce on the rebound of Ayoube Amaimouni-Echghouyab’s initial shot to fire into the top corner.
But Koln replied almost immediately when Kamiński powered through the heart of the Frankfurt defence and placed his finish past Zetterer.
The visitors continued to push for an equaliser, and René Wagner’s substitutes combined for it with just over five minutes left.
Luca Waldschmidt’s header on allowed Marius Bulter to play it across goal, where Alessio Castro-Montes arrived to tap in just seconds after coming on.
Neither side was able to find a late winner, meaning Frankfurt now have a 10-point gap to make up to the top six, while Koln teeter just two points from the relegation play-off spot after winning just two of their last 19 Bundesliga matches.
Flashscore Man of the Match: Jakub Kamiński (Koln)