Cologne, without a win now in the last 14 Bundesliga matches, conceded a penalty at the end of a low-key first half with Andre Silva putting the visitors in front.
It only lasted seven minutes as Ondrej Duda equalised with a fine shot in what was the hosts' first chance of the entire game in the 52nd minute.
Duda had a rare good chance for the hosts but his diving header from 12 metres was tipped wide by keeper Kevin Trapp.
The result left Frankfurt in fourth place on eight points. For Cologne it was the first point of the season but kept them in 16th place.