The midfielder's 33rd-minute strike maintained Belgium's unbeaten run in Group E as they advanced to 16 points, nine points ahead of the Czech Republic, who have played one game fewer, and Wales, who have two games in hand.
Praet steered a snap effort wide of Belarus goalkeeper Sergei Chernik after being teed up by a short pass from Alexis Saelemaekers, two minutes after Michy Batshuayi had the ball in the net but his effort was ruled offside.
Belgium, top of the FIFA rankings, scored eight goals against Belarus at the start of the World Cup qualifiers in March but this time looked tired after a third game in six days, having beaten Estonia and the Czech Republic in their previous two qualifiers.
They were without suspended Romelu Lukaku and Jan Vertonghen and elected to spare Thibaut Courtois, Yannick Carrasco and Axel Witsel the long trip to Russia, where Belarus were forced to host the game because of flight sanctions.
Captain Eden Hazard started on the bench and only came on after an hour but failed to provide the expected spark. His free kick four minutes from fulltime, however, did force a sharp save out of Chernik.
Belarus, who did not trouble Belgium in the game, have now lost four of five qualifiers and sit second from bottom in the group.