The 19-year-old striker Jesus, who has scored three goals in five games since joining City in January, suffered a "fractured metatarsal" bone against Bournemouth on Monday. He was brought off in the 15th minute of the 2-0 win which lifted City to second in the Premier League.
City did not say how long Jesus would be sidelined. "He will undergo further examinations in the coming days to establish the extent of his layoff," said a club statement.
British media reports said Jesus underwent a scan on Tuesday that revealed the fracture. He was pictured walking in Manchester with a protective boot.
City paid Brazilian club Palmeiras an initial £27 million ($33 million/31 million euros) for Jesus.
The striker scored at West Ham and twice against Swansea and Jesus was hoping to become the third City player -- after Emmanuel Adebayor and Kevin de Bruyne -- to score on each of his first three Premier League starts.
City manager Pep Guardiola said after the Bournemouth game that he was "praying" the damage would not be serious.
The Brazilian's impact has been so dramatic that reports had said Argentinian striker Sergio Aguero could leave.
Aguero came on to replace Jesus at Bournemouth and is now set to reclaim his place as number one striker.
The injury is a particular blow to City as the Premier League campaign intensifies and they meet Monaco in the Champions League last 16 first leg next week.
Medical experts say that on average, a broken metatarsal needs about eight weeks recovery. Manchester United striker Wayne Rooney has had a broken metatarsal three times and needed between six weeks and three months to return.
Doctors recommend four to eight weeks rest. The treatment depends on the extent of the damage.
If the foot is bad enough to warrant being put in plaster, he would have to keep the cast for four to six weeks.
Jesus would then make a gradual return with exercises to increase the strain he can put on the foot. The return could be another four weeks or more.