Although this collision saw the lowest seed in the round host the highest, it was the first to have the early stock exchanges better.
The Greek international Christos Tzolis tested Rui Patricio in the Atalanta goal twice in the opening 10 minutes, but these were just warning shots that were not detected by La Dea.
At the quarter of the quarter, Stefan Posch was far too casual in receiving a pass from Isak Hien and was picked by Chemsdine Talbi, who fed Ferran Jutgla and allowed him to emphatically end his nine-game goals drought and the to open score.
The holders of the UEFA Europa League struggled to get a foothold in a raw Jan Breydel Stadium when home captain Hans Vanaken managed to deviate from the free kick delivery of Maxim de Cuyper.
Nicky Hayen's side has done well to keep one of the most popular attacks in Europe during the first 40 minutes, but the head coach will be disappointed by the way in which the equalizer of Atalanta is less than five minutes before the break .
Davide Zappacosta was given too much time to deliver a cross from the left and therefore chose the totally unark Mario Pasalic, who came up for a header home.
The second half started just like the first, with the hosts on the front foot and Atalanta, sometimes somewhat confused.
However, the Blau-Zwart could not really bother Patrício. Their lack of creativity almost came back to chase them when the men of Gian Piero Gasperini came twice close to completing their comeback halfway through the second period.
First the deep cross of Juan Cuadrado was replaced by Zappacosta, but Simon Mignolet came over to cover. Almost immediately afterwards, fellow replacement Lazar Samardzc should have done better as a one-on-one with the Bruges goalkeeper, but all the calmness lost and his efforts widely dragged.
Graduated Bruges Academy and the local boy Charles de Ketelaere had been quite quiet until he was well connected to Samardžić within the last 10 minutes and the Palmen Mignolet stung from the edge of the box.
Both parties insisted on a goal that would give them the benefit, and it was the Belgian outfit that had the opportunity to do this by referee Halil Umut Meler in stopping time.
Hien was perplex when Meler pointed to the place after the defender's hand was connected to countryman Gustaf Nilsson, and the big attacker picked up before Patricio sent the wrong direction.
This result means that Atalanta has now only won one of their last five games in all competitions, and they now have a lot of work to do in home if they want to make the last 16.
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