The 42-year-old Englishman was appointed at the end of December 2022 but won just two of his 12 matches in charge of the reigning Belgium champions.
Brugge lost the second leg of their UEFA Champions League round of 16 tie 5-1 to Benfica on Tuesday, culminating in a 7-1 aggregate defeat.
That loss has proven to be Parker's final game in charge.
It is the second time the former England midfielder has been sacked this season after Bournemouth showed him the exit four games into the 2022/2023 Premier League campaign. On that occasion, a 9-0 loss to Liverpool was the catalyst for his dismissal.
Brugge were brutal in their statement announcing the former Chelsea and West Ham United midfielder's exit, which read: "Scott Parker is no longer head coach of Club Brugge.
"Parker was appointed as Club Brugge's new head coach on December 31, replacing Carl Hoefkens. Before coming to Jan Breydel [Stadium], the former England international was at the helm of teams like Fulham and Bournemouth. Parker won two of his 12 games for Club."
Parker leaves Club Brugge fourth on the Belgium league table, 21 points behind leaders Genk.
