Frankfurt was knocked out 2-1 from Freiburg at home in the final line-up of the Spanish giant Barcelona quarter-finals in Barcelona on Sunday.
Frankfurt striker Filip Kostic equalized after Vincenzo Grifo gave Freiburg an early lead before Nils Petersen headed in the visitors’ late winner.
It was a disappointing result for Frankfurt, four days before their Europa League quarterfinal, second leg at Barcelona’s Camp Nou having drawn the home tie 1-1 last Thursday.
Sunday’s league win is a significant boost for Freiburg in their bid to reach the Champions League next season.
With five games left, they drew level on 48 points with fourth-placed RB Leipizg with the top four clubs qualifying for the Champions League.
There was a brief delay at the start of the first half when two environmental protestors each tied themselves to a post in the Frankfurt goal.
After Kostic’s equalizer ruled out Grifo’s opening goal, Petersen came off the bench to head in the winner from a free-kick on 69 minutes.
Frankfurt thought they had equalized again when Japan midfielder Daichi Kamada hit the bottom corner late on, but VAR ruled he was offside.
Minutes before, Frankfurt replacement forward Ajdin Hrustic had hit the post as the hosts pushed for a second goal.
Earlier, a slip while taking a penalty cost France winger Moussa Diaby the chance to score as Bayer Leverkusen was held to a goalless draw at Bochum.
Leverkusen, who remains third, was awarded a penalty when Czech Republic striker Patrik Schick went down in the area midway through the second half.
Diaby stepped up to take the spot-kick but slipped striking the ball, which flew into the net only after rebounding off his standing leg.
The referee spotted the second touch and disallowed the goal.
The result leaves Leverkusen trailing 17 points behind runaway league leaders Bayern Munich, who inched towards a tenth straight Bundesliga title on Saturday with a 1-0 home win over Augsburg.