Kevin De Bruyne added a third goal in stoppage time as a full-strength Belgium side, who top the FIFA rankings, dominated the Scots from the start.
Yet the likes of De Bruyne and Eden Hazard were unable to make a breakthrough until right on halftime, when Hazard scooped the ball up in the air from the byline for Lukaku to head home.
The Manchester United striker then netted his 48th international goal as he followed-up a shot by De Bruyne that was parried into his path by Scotland goalkeeper David Marshall in the 57th minute.
Lukaku put two efforts narrowly wide as he went in search of his hat-trick while Scotland could have pulled one back on a rare counter attack in the 85th minute.
Yet even with Belgium keeper Thibaut Courtois out of position, the ball got stuck between the legs of first Ryan Fraser and then Oliver Burke and the opportunity was lost.
Russia are second in the group with nine points after beating Cyprus 1-0 in Nizhny Novgorod with Aleksey Ionov scoring in the 38th minute.
The narrow margin of victory contrasted with the 9-0 home win they had over San Marino on Saturday.
Earlier on Tuesday, Kazakhstan beat San Marino 4-0 for a second win in the group, although it took them until just before halftime to break the deadlock.
(Reporting by Mark Gleeson; Editing by Toby Davis)
