Fans were left shocked by the decision, with one saying: "Might be the worst decision I've seen all season.".
Fuming Atalanta stars surrounded the referee, with Rafael Toloi, ex-Chelsea man Juan Cuadrado and Hien all getting yellow carded.
Atalanta boss Gian Piero Gasperini stormed down the tunnel as the ball hit the back of the net, ripping his coat off as he went.
The striker chased down a loose ball in the box, only for Atalanta defender Isak Hien to get there first and hold him off.
Club Brugge scored a 94th minute penalty to beat Atalanta 2-1 in a first leg play-off round clash.
