The 19-year-old Brazil striker limped out of City’s Premier League win at Bournemouth on Monday after just 15 minutes and underwent tests on Tuesday morning.
The club are unsure how long the player will be sidelined but there are fears he could be out for up to three months.
A statement from the club read: “Manchester City can confirm Gabriel Jesus suffered a fractured metatarsal during the 2-0 win over Bournemouth on Monday night.
“He will undergo further examinations in the coming days to establish the extent of his lay-off.”
The news is a blow for City, who resume their Champions League campaign next week as Monaco visit the Etihad Stadium in the first leg of their last-16 tie.
Jesus has made an immediate impact at City after joining the club in £27million deal from Palmeiras in January.
He has scored three goals in his five appearances, including an injury-time winner against Swansea, and so impressive were his performances he was being selected ahead of top scorer Sergio Aguero.
That situation had sparked fresh speculation over the future of Aguero, who has scored 154 goals for City since joining the club in 2011.
Aguero, 28, replaced Jesus at the Vitality Stadium and forced the Tyrone Mings own goal which saw City complete their 2-0 victory and move to second in the Premier League.
The Argentina international is now likely to continue leading the line, although City are not in Premier League action again until March 5. They travel to Huddersfield in the fifth round of the FA Cup this weekend.
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