The defender netted in the 70th minute, with the Red Devils going on to win 2-1, making them the first European side to join hosts Russia at the finals with two qualifying games in Group H still to play.
Jan and Toby Alderweireld both played the full game, while Mousa Dembele also started before being substituted with 16 minutes left.
Group A leaders France, with Hugo Lloris between the sticks, were held to a goalless draw at home by Luxembourg while Vincent Janssen played 90 minutes for the Netherlands as they moved up to third in the same group with a 3-1 home win over Bulgaria.