Bruges, who have now won 15 titles, came back after conceding early to equalise three minutes before halftime but Ruud Vormer handled the ball before setting up Jelle Vossen for the goal.
The referee consulted the Video Assistant Referee (VAR) after the incident but still awarded the goal to the disbelief of the home supporters.
Cypriot international Konstantinos Laifis’ 11th minute goal had given Standard early hope they might take the title race into the last round of matches next Sunday.
Standard, who started four points adrift with two matches to play, remain on course for second place and a spot in the preliminary rounds of next season’s Champions League after third placed Anderlecht were beaten 1-0 at Ghent.
Bruges moved onto 46 points with Standard on 42 and Anderlecht on 40.
(Reporting by Mark Gleeson in Cape Town; Editing by Toby Davis)
