Freiburg had led following their 1-0 victory a week ago, but they toiled in the Slovenian capital Ljubljana, where Domžale are having to play their home European matches.
Senijad Ibričić levelled the tie from the spot early in the second half, with Lovro Bizjak scoring what turned out to be the winner shortly afterwards.
Bizjak and Niederlechner close in goalless first 45
Nils Petersen had given Freiburg their narrow 1-0 lead from the first leg, although they missed several opportunities, especially late on, to impose their dominance on the tie. That left things firmly in the balance, with only one German side (Borussia Dortmund) having progressed into the group stages in the previous four seasons.
With just one change to the starting line-up, Aleksander Ignjovski replacing Tim Kleindienst, they looked to pick up here where they left off, although Pascal Stenzel and Petersen, via a deflection, went wide early on.
Their Slovenian hosts though, more so than a week ago, began to pose a real threat. An early effort went over from Bizjak, and he would prove more dangerous later on. Hustling off Philipp Leinhart, he gave Amedej Vetrih the chance to strike just wide, before himself cutting in from his berth on the left to put the ball over the bar.
The two teams reached an impasse after that. Florian Niederlechner recorded a rare shot on target before putting a free-kick wide, however he would have the best chance of the half just before the break. Receiving the ball from Stenzel, he struck hard into the Domžale goalkeeper Dejan Milić. He couldn’t hold at first, the ball hitting Petersen on the face, before the keeper could clean it up at the second attempt.
Ibričić and Bizjak end Freiburg’s European adventure
It all started to go wrong for Christian Streich’s men soon after the break. Çağlar Söyüncü gave away a penalty after catching Matija Širok inside the box, abruptly halting what was turning into a dangerous attack. Ibričić sent Alexander Schwolow the wrong way from the spot, his penalty tucked in on the left post. The hosts led on the night and it was all square on aggregate.
Freiburg immediately went about trying to regain their overall lead. Niederlechner fired wide after a ball was played across to him by Petersen, before they swapped roles for an even better opportunity. Getting the better of a defender, Petersen only had Milić to beat but the keeper blocked with his feet.
Then came the hammer blow. Zeni Husmani played a good ball to Ivan Firer on his left, the striker charging forward before putting the ball across for Bizjac to slide in and beat Schwolow, leaving Freiburg facing exit from Europe at the first possible hurdle.
An away goal was all they needed, however the opposite looked far more likely. Ibričić had a shot put wide by Schwolow, before Gaber Dobrovoljc rose highest the head the subsequent corner into the bar, Schwolow having no chance of saving it. Freiburg were offering little to response – Petersen and Kleindienst had chances, but their side’s European challenge ultimately petered out with a whimper.