Raio Piiroja opened the scoring for the hosts on the half-hour mark and Konstantin Vassiljev secured the win with Estonia's second midway through the second period. The home side went on the attack from the off and Kaimar Saag almost gave them a 10th-minute lead with a shot which grazed the bar.
Belgium offered little as an attacking threat in the opening half, with Roland Lamad having their best chance, his thunderous shot striking the upright. Estonia took the lead after 30 minutes when Konstantin Vassiljev whipped in a cross and defender Piiroja rose highest to plant his header past Logan Bailly.
Belgium's Dutch coach Dick Advocaat made two substitutions at the break, dragging off Daniel van Buyten and Gaby Mudingayi and replacing them with Toby Alderweireld and Thomas Buffel. The Red Devils controlled possession following the restart but it was Estonia who offered the greater threat in front of goal.
The Estonians extended their lead after 67 minutes. Joel Lindpere won the ball in midfield before laying it off to Dmitri Kruglov and his cross was controlled neatly by Vassiljev, who then swept the ball home.
Belgium poured forward in the closing stages in a bid to salvage something from a disappointing display. However, despite some long spells of pressure they found goalscoring chances hard to come by.