
The result leaves Atletico 14th in the league phase standings on six points from four matches, level with five other teams, while Belgium champions Union Saint-Gilloise sit 26th with three points and outside the qualification spots.
Union Saint-Gilloise started aggressively, exploiting counter-attacks with speed, but Atletico struck first in the 40th minute when Giuliano Simeone burst up the right channel and put it on a plate for his Argentina team mate Alvarez to unleash an unstoppable half-volley from inside the box.
Atletico came off the break livelier and finally found their second goal in the 72nd minute when Gallagher fired a bullet strike from inside the box, grabbing a loose ball when the defenders failed to clear it away in a quick counter by Alexander Sorloth.
Union Saint-Gilloise refused to go quietly, cutting the deficit in the 81st minute when Sofiane Boufal sent a cross from a free kick at the left to the far post where Ross Sykes leaped high to unleash a towering header into the bottom left corner.
The goal set up a nervy finish for the hosts who finally managed to score again when Llorente made it 3-1, striking home a rebound from inside the box in the last minute of added time.