While this clash saw the lowest seed in the the round host the highest, it was the former who had the better of the early exchanges.
Greek international Christos Tzolis tested Rui Patricio in the Atalanta goal twice in the opening 10 minutes, but these were merely warning shots that were not heeded by La Dea.
On the quarter-hour mark, Stefan Posch was far too casual in receiving a pass from Isak Hien and was pickpocketed by Chemsdine Talbi, who fed Ferran Jutgla and allowed him to finish emphatically to end his nine-game goal drought and open the scoring.
The UEFA Europa League holders struggled to gain a foothold at a raucous Jan Breydel Stadion as home captain Hans Vanaken had an effort deflected just wide from Maxim De Cuyper’s free-kick delivery.
Nicky Hayen’s side did a good job of keeping one of Europe’s hottest attacks quiet during the first 40 minutes, but the head coach will have been disappointed by the manner of Atalanta's equaliser less than five minutes before the break.
Davide Zappacosta was given too much time to deliver a cross from the left and therefore picked out the totally unmarked Mario Pasalic, who rose to flick home a header.
The second half began much like the first, with the hosts on the front foot and Atalanta, at times, looking somewhat flustered.
However, the Blau-Zwart were unable to really trouble Patrício. Their lack of creativity almost came back to haunt them when Gian Piero Gasperini’s men twice went close to completing their comeback midway through the second period.
First, substitute Juan Cuadrado’s deep cross was met by Zappacosta, but Simon Mignolet got across to cover. Almost immediately afterwards, fellow replacement Lazar Samardzc should have done better when one-on-one with the Brugge goalkeeper, yet lost all composure and dragged his effort wide.
Brugge academy graduate and local boy Charles De Ketelaere had been fairly quiet throughout until linking up well with Samardžić inside the last 10 minutes and stinging the palms of Mignolet from the edge of the box.
Both sides continued to push for a goal that would edge give them the advantage, and it was the Belgian outfit who were gifted the opportunity to do so by referee Halil Umut Meler in stoppage time.
Hien was perplexed when Meler pointed to the spot after the defender's hand had connected with compatriot Gustaf Nilsson, and the big forward picked himself up before sending Patricio the wrong way.
This result means Atalanta have now won just one of their past five matches in all competitions, and they now have plenty of work to do on home soil if they want to make the last 16.