The 19-year-old made a blistering start to his Man City career with three goals and an assist in his first three games, but he lasted just 15 minutes of Sunday's 2-0 win over Bournemouth before being forced off.
Guardiola revealed that the Brazilian is expected to miss up to three months with the problem, which could mean that he does not feature again until the 2017-18 campaign.
"I don't know if Gabriel Jesus will play again this season. They say [he could be out for] two or three months," he told reporters.
The injury means that Sergio Aguero is likely to regain his starting place in the team, and Guardiola insists that he has full confidence in the Argentine despite recently dropping him to the bench.
"It's not easy for the player who does not play. Sergio was more than professional. I don't have doubts about Sergio. He has to do what he has done since the beginning of his career. Nothing more," he added.
City take on Huddersfield Town in the FA Cup on Saturday looking for a fifth straight win in all competitions.