The visitors needed only to avoid defeat to be sure of qualifying as winners of Group A but got across the line with plenty in reserve as Croatia - who replied late on through Niko Kranjcar - had to be content with a place in the play-offs.
Marc Wilmots' star-studded Belgians have cruised through their qualification campaign, with Friday's 2-1 win their eighth of the group stage - their only dropped points so far coming with a draw at home to Croatia in September last year.
Even without the injured Vincent Kompany and Christian Benteke Wilmots was able to field a line-up with quality in every area, with the likes of Jan Vertonghen, Axel Witsel, Marouane Fellaini and Eden Hazard all on show.
But it was Everton striker Lukaku who took centre stage in the first half, bagging two more goals in what has been a fine start to the season to further call into question the decision of Chelsea manager Jose Mourinho to ship him out on loan.
Sixteen minutes had gone when the giant frontman opened the scoring, Steven Defour providing a defence-splitting pass that he ran onto before rounding the goalkeeper and slotting home.
Croatia goalkeeper Stipe Pletikosa did better on 28 minutes when he clawed away a Fellaini header, but he had no answer 10 minutes later when Lukaku made it two.
This time the striker got in behind the home defence and benefited from a lucky ricochet as Pletikosa dived at his feet, the ball bouncing into his path and allowing him to run the ball into the unguarded net.
Croatia rallied just before the break and Belgium had Thibaut Courtois to thank for preserving their clean sheet when he reacted to keep out Mario Mandzukic's header.
The second half lacked the excitement of the first, with Croatia perhaps resigned to their fate.
However, the visiting fans did have reason to get to their feet in the 69th minute as they acclaimed match-winner Lukaku, who was withdrawn to be replaced by Nacer Chadli.
Belgium almost made it three 13 minutes from the end when substitute Kevin Mirallas played in Fellaini but the Manchester United man saw his low shot kept out by the feet of Pletikosa.
Instead the final goal went the way of the hosts as Kranjcar drilled home a sweet half-volley with six minutes left, but Belgium were not to be denied the pleasure of sealing their first World Cup appearance since 2002 with a fine victory.