Atalanta looked to be escaping Bruges with a draw after Mario Pasalic's fine header four minutes before half-time levelled Ferran Jutgla's fabulous opener for the hosts.

But Nilsson won and then netted the decisive penalty at the Jan Breydel Stadium, delighting home fans and enraging Atalanta who could barely believe that the spot-kick had even been awarded.

Atalanta coach Gian Piero Gasperini stormed down the tunnel before the final whistle in anger while his players continued to protest at the end of the match, collecting only a series of bookings from unrepentant referee Umut Meler.

Nilsson had crumpled to the turf after being grazed on the face by Isak Hien's left fingers as the Atalanta defender ran to collect the ball in his own area.

Hien couldn't believe his eyes when Meler pointed to the spot and gave Nilsson the chance to fire Club Brugge to a win which they might have otherwise deserved for their enterprising performance in front of passionate home support.

"All I could see is that he (Meler) was arrogant, if you tried to speak to him he just handed out yellow, yellow, yellow," said Charles De Ketelaere whose return to his home town and boyhood club was marred by the late penalty drama.

"I've only just seen the footage and I reckon that if you ask 100 people if that was a penalty all 100 would say no. It's very strange.

"It hurts to lose right at the end like that. And it's definitely not right."

Club Brugge take a slender lead to next Tuesday's second leg in Bergamo where Atalanta will be fired up to go through and face one of Aston Villa or Lille in the next round.

Penalty anger 'pointless

But the Serie A team will have some work to do get through, as they battle injuries, including key attacker Ademola Lookman, and were clearly rattled by their opponents at various points in the match.

"It's pointless to talk about the penalty, I think anyone who watches football knows that was never a penalty," said Marten de Roon.

"But what we need to do is look at our performance today which was not good... we need to be better if we want to get through."

Club Brugge tore into the sluggish away side from the first whistle, doing to Atalanta what Atalanta usually do to other teams with intense pressure and high energy in chasing down the ball.

Atalanta were off the pace and it was an uncharacteristic mistake from Hien which led to Jutgla's opener, with Chemsdine Talbi pouncing on a sloppy pass before setting up his Spanish teammate for a fine finish.

But moments before the break Pasalic struck the leveller in the only short period of the match in which Atalanta were on top.

Brugge again came out all guns blazing after the break but although Gasperini was left baffled by Atalanta's performance it was his team that created the two best chances of the game around the hour mark.

First Simon Mignolet did brilliantly to keep out Davide Zappacosta's close-range header and then substitute Lazar Samardzic  blasted well wide a great chance to put Atalanta in the lead with the goal at his mercy.

That appeared to be it until Nilsson hit the deck and Meler gave Club Brugge a penalty which could be decisive in the tie.