In a game that Belgian officials said was nearly called off after a terrorism scare, Lukaku scored with the easiest of headers at the far post from Nacer Chadli's cross to take his tally to 31 goals in 65 appearances.
Belgium extended their unbeaten run to 15 games, their last defeat having come against Spain in a friendly in September last year.
The Belgian football association, quoted by public broadcaster RTBF, said that in the end there had been no danger to the public, although extra security measures, including metal detectors, meant many fans were late taking their seats.
Bruges police told local media they had been warned by the federal authorities shortly before the kick-off of a possible attack during the match, prompting the additional checks.
Belgium has been on high alert since Brussels-based Islamic State militants attacked Paris, including a France-Germany soccer friendly in the city, two years and one day ago. Brussels itself was attacked by IS suicide bombers in March last year.
(Additional reporting by Alastair Macdonald in Brussels; Writing by Brian Homewood in Berne; Editing by Toby Davis)
