City boss Pep Guardiola said Haaland noticed the injury after Wednesday's defeat at Aston Villa.
The Norway striker's absence from the trip to Kenilworth Road is a big blow as City try to keep pace with leaders Liverpool.
Haaland set the Premier League's single-season goal record last term and has scored 19 times in the current campaign.
Guardiola will be sweating on Haaland's fitness with City travelling to the FIFA Club World Cup in Saudi Arabia before returning for the busy festive programme.
"A bone stress reaction in his foot and after the last game he felt it. He cannot play," Guardiola said just before kick-off at Luton.
"I don't know (the length of the injury). Week by week, day by day, we will see what happens."
Guardiola continued: "We play with 11 that's for sure. Erling has been so important since he's arrived that's for sure. But during the season we see this sort of thing. Injuries, suspensions, problems, we have to adapt."
