In action for Mouscron was former Nigeria junior international Taiwo Awoniyi who played for 90 minutes.
Massimo Bruno gave Anderlecht the lead in the 42nd minute but Omar Govea equalised for Mouscron in the 52nd minute.
But with 10 minutes remaining, Onyekuru scored what proved to be the winner for Anderlecht.
Onyekuru, who is on loan from Everton, has now scored seven goals in 14 league appearances in the Belgian first division.
Anderlecht are now third on 28 points, six points behind leaders Club Brugge.