Referee Robias Stieler awarded a penalty after Tyrone Mings, who was making his first appearance in the competition, was caught off guard while receiving a back pass from Emi Martinez inside his own penalty area.
Hans Vanaken stepped up to convert from the spot and end his side's 14-game run without victory against English opposition.
The penalty decision followed an underwhelming first half from Villa, who were subject to an onslaught from the Belgian champions. Brugge had seen an effort from Vanaken pushed onto the post before Martinez reacted quickly to the follow-up to keep out the ball in what was a busy first 45 minutes for the goalkeeper.
Despite Villa dominating the early possession statistics, Brugge had dominated the chances, with Unai Emery's Villans only managing a single effort on target before the interval compared to five from the home side.
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cookies for this session only. Enable CookiesAllow Cookies OnceThe only opportunities for Villa before the break came as John McGinn headed over a Boubacar Kamara cross from close range and a wayward strike from the edge of the Brugge area from Ollie Watkins whistled wide.
Emery called on intervention from the bench with Jhon Duran introduced hoping to add to his tally of two vital goals in the competition thus far but the striker failed to make an impact.
Defeat for Villa means Liverpool remain the only side with a 100-per-cent record in the competition. Emery's side have now gone four consecutive games without victory in all competitions, losing all of their last three.
More to follow.