Jutgla worked relentlessly throughout the match to help link the defense and attack and capped his display with an assist and a goal.
The 23-year-old Jutgla has been one of the revelations of the season after joining from Barcelona, where he struggled for playing time.
At Brugge, he has been making the most of the freedom of movement he enjoys in the system set up by coach Carl Hoefkens, scoring eight goals and delivering five assists in all competitions.
On Tuesday, Jutgla created the move that led to Kamal Sowah’s opening goal in the 36th minute and made it 2-0 after the hour-mark.
Goalkeeper Simon Mignolet was also flawless, making a number of saves to keep Atletico at bay.
It was Brugge’s 14th overall Champions League match win, surpassing the Belgian record of Anderlecht. Brugge leads Group B with nine points, six more than Porto, Leverkusen and Atletico.
Brugge enjoyed most of the possession early on and used a strong press to quickly recover the ball when they lost it.
Playing in its usual 4-4-2, with Antoine Griezmann and Alvaro Morata up front, Atletico waited for an opening but couldn't capitalize when they arrived.
The Spanish side had a first chance in the seventh minute when Cedric Carrasco’s shot took a deflection to sail over the bar, and Griezmann forced Mignolet to parry away his shot from a tight angle 10 minutes later.
Morata then found himself alone for a one-on-one with Mignolet but the former Liverpool keeper kept his team afloat with another fine save, this time with his feet.
And when Brugge looked like it was close to cracking, a beautiful move between Jutgla and Sowah broke the stalemate. After Hans Vanaken cleverly headed the ball into his path, Jutgla played a quick one-two with Sowah then dribbled past the Atletico defense before crossing the ball for his teammate, who tapped the ball in.
Jutgla came back from the halftime break with the same intentions and after chesting down a pinpoint cross from the right near the penalty spot, the Spanish forward fired an instant shot that Jan Oblak kept out with his left arm.
Oblak could not stop Brugge's next move, again initiated by Jutgla. Following a one-two with Buchanan, the Spaniard was clinical from inside the box to make it 2-0 with a side-footed shot.
Atletico was awarded a penalty with 15 minutes left but Griezmann hit the crossbar and Mignolet made two more saves in the 89th and 90th.
“What we missed today was forcefulness, in the first half we had a few chances where we could have done more,” said Atletico captain Koke. “In the second half we had more chances and the penalty but it wouldn’t go in.”