Goals from Eder Balanta and Federico Ricca helped the Blue-Black survive the hosts scare after going behind first.
Yohan Boli gave St. Truiden the lead after converting Santiago Colombatto’s assist in the 20th minute.
However, the visitors equalised in the 44th minute through Balanta who fired past Daniel Schmidt thanks to Angola’s Clinton Mata.
With five minutes left to play, Ricca sealed the win to earn Club Brugge their 13th win out of 17 fixtures.
South Africa’s Percy Tau featured for nine minutes after replacing Siebe Schrijvers in the 81st minute, while Nigeria’s Emmanuel Dennis saw a minute of action.
Philippe Clement’s men lead the league table, and they will now shift their attention to Wednesday’s Champions League clash against Real Madrid.
Club Brugge need a win to earn a place in the Europa League after blowing away their chance of progressing in Europe’s elite club competition with a 1-1 draw at Galatasaray on November 26.