Frankfurt started the game without talisman Omar Marmoush, who is in discussions over a move to Manchester City, but the hosts began brightly here.
Visiting goalkeeper Gregor Kobel stuck out a leg inside the opening minute to deny Hugo Larsson, atoning for a slack pass intended for Pascal Groß that had been seized on by Ellyes Skhiri.
Dortmund gradually grew in belief, with Julian Ryerson’s lofted cross headed against the woodwork by Serhou Guirassy, but their defensive fragility was soon on full display.
In the 18th minute, Rasmus Kristensen found Hugo Ekitiké, who played an inviting reverse pass for the Dane to race on to, before the striker charged upfield and tucked home Kristensen’s cross.
Frankfurt could soon have made it 2-0 as former Dortmund players Mario Götze and Ansgar Knauff combined, with the latter rattling Kobel’s left-hand post from the edge of the box before Dortmund head coach Nuri Şahin introduced Yan Couto in place of Ramy Bensebaini at half time.
Couto quickly made an impact, with Frankfurt goalkeeper Kevin Trapp repelling the Brazilian’s close-range shot before the right-back’s teasing cross just evaded Guirassy.
Nnamdi Collins, who avoided giving away a penalty in the first half for a challenge on Guirassy, was then lucky not to concede a spot-kick with around 15 minutes of normal time remaining after barging Jamie Gittens in the back.
Guirassy was the next to go over in the box after contact was made by Arthur Theate, only for the striker’s appeals to be waved away.
Frankfurt ultimately closed out the contest as Emre Can was dispossessed, allowing Oscar Højlund to complete the job, while the commanding performance of centre-back Robin Koch was also instrumental in earning the victory.
This marks the first time that Dortmund have failed to score in a Bundesliga game since August as they remain 10th ahead of a pivotal UEFA Champions League encounter at Bologna next Tuesday.
Meanwhile, Frankfurt also have European duties next week, as they welcome Ferencváros to Deutsche Bank Park on Thursday, looking to stay in the top eight of the UEFA Europa League table.
Flashscore Man of the Match: Robin Koch (Eintracht Frankfurt)