While head coach Roberto Martinez initially hoped Lukaku would be able to face Cyprus on Sunday, Belgium confirmed the striker would miss the trip.
"@RomeluLukaku9 will not travel with us to Cyprus this morning due to a foot injury," they wrote on Twitter on Saturday.
"Get well soon, Romelu!"
Lukaku last played competitively during United's 2-0 loss to Arsenal on March 10.
Without him, Belgium got past Russia thanks to an Eden Hazard brace and a Youri Tielemans strike, and they will be aiming for a second win in Group I when they visit Cyprus.
However, it is likely his club that will be more anxious to see the frontman make a swift recovery.
United are already without Alexis Sanchez, while Anthony Martial and Marcus Rashford both withdrew from international duty with injuries, leaving Ole Gunnar Solskjaer desperately short of options at centre-forward.
The Belgian joins a mounting injury list for the Norwegian to contend with that also includes Luke Shaw and Nemanja Matic, while Phil Jones, Antonio Valencia, Marcos Rojo and Matteo Darmian are all short of match fitness.
Solskjaer will hope that some of the names on that list will be available for selection when club football resumes, as United look to put back-to-back defeats behind them when they host Watford at Old Trafford in the Premier League as the fierce fight for a top-four finish resumes.