Manchester United forward Lukaku scored once in each half to make it 25 international goals in his last 21 appearances and in truth he should quite conceivably have finished with four or five to his name.
Kevin De Bruyne sealed the win with a 20-yard strike in stoppage time as Steve Clarke suffered his first defeat as Scotland manager and his side now sit three points behind second-placed Russia.
Belgium dominated a first half that saw the visitors squander their only chance through Oliver Burke and lose Stuart Armstrong to injury, with away goalkeeper David Marshall saving well from De Bruyne early on.
Another effort from De Bruyne was wonderfully tipped away from the top corner by Marshall, before the Manchester City star laid on a great close-range chance for Lukaku that the striker somehow managed to block with his own foot.
But Lukaku made up for that one minute into first-half stoppage time, rising above Scott McKenna to thump in a header from six yards after Eden Hazard had linked up with his brother Thorgan and floated in a clever cross.
Lukaku could not convert a superb headed chance early in the second half, while De Bruyne's free-kick was saved by Marshall.
But the powerhouse striker got his second after 57 minutes, tapping in a rebound after Marshall tipped away an effort from De Bruyne, who Scotland claimed was offside in the build-up.
Lukaku twice fired just wide as he sought a hat-trick, while Thibaut Courtois confirmed his clean sheet with a key late save from McKenna before De Bruyne netted after a neat exchange with substitute Dries Mertens to give the scoreline a more realistic look.