The Belgian champion made it three Group B victories out of three at Jan Breydel Stadium to move another step closer to securing a surprise spot in the last 16.
Soweh was on target in the first half and Jutgla doubled the lead for Carl Hoefkens' side, which is six points clear at the summit.
Antoine Griezmann missed a penalty as Atleti suffered a defeat that leaves it bottom of the group, but level on three points with Porto and Bayer Leverkusen with three matches to play.
The early signs were promising for the LaLiga side, with Griezmann forcing a save from Simon Mignolet with the best chance of the first quarter.
But Brugge shrewdly grew into the match, and when Sowah nudged home Jutgla's cross from close range, it had the lead 36 minutes in.
The Spanish side made a bright start to the second half, but Jutgla stunned them by rifling home after the visitor failed to clear.
A spot-kick for a foul on Matheus Cunha presented a route back into the match, but Griezmann's effort struck the woodwork, summing up a poor night for Diego Simeone's men.