Roberto Martinez's men were predictably in control throughout the Group E encounter, Christian Benteke's simple finish putting them on course for victory inside a quarter of an hour.
The Red Devils peppered the Estonia goal to no avail for the rest of the first half before Yannick Carrasco, having played a part in the opener, thrashed home a second in the 53rd minute.
Erik Sorga pulled one back for the group's second-bottom side but Thorgan Hazard, after replacing brother Eden, restored Belgium's two-goal advantage, their five-point lead at the summit ensuring it will be at the finals in Qatar, which begin next November.
Estonia could only delay the inevitable until the 11th minute as Benteke tapped in after Matvei Igonen spilled Carrasco's pull back after a stunning ball from Kevin De Bruyne.
De Bruyne saw a free-kick superbly turned onto the post by Igonen before Benteke was frustrated by the woodwork and then Igonen as Belgium piled on the pressure.
The instrumental De Bruyne sent Eden Hazard through on goal with a magnificent pass with the outside of his boot, but the Real Madrid man failed to round Igonen, who made a fine smothering stop.
But Igonen could do nothing to stop a swerving long-range effort from Carrasco nestling in the top corner to give Belgium the measure of command their performance merited.
Estonia did produce an unexpected reply, Sorga pouncing on the rebound after Thibaut Courtois could only parry Rauno Sappinen's drive.
It was fittingly De Bruyne that made sure Belgium had the final say as his perfectly weighted cross to the far post was nodded home by Thorgan Hazard, further gloss to the scoreline from Alexis Saelemaekers removed by the offside flag.