The Brazil striker removed his right boot and received treatment on the field before making way for Sergio Aguero at the Vitality Stadium.
Raheem Sterling opened the scoring before the half hour and the England winger turned provider in the 69th minute, with Bournemouth defender Tyrone Mings putting through his own net under pressure from Aguero.
City moved up to second in the table, within eight points of leaders Chelsea, but the post-match focus understandably turned towards Jesus.
"Tomorrow [Tuesday] morning we will know exactly," Guardiola told Sky Sports.
"He was so, so unfortunate. Hopefully – I'm am going to pray tonight – it is not going to be a big issue."
The 19-year-old's injury gave Aguero a chance to impress after two weeks where his emergence cast doubt on the long-term future of City's top scorer.
Guardiola was unaware his team's second goal was credited to Mings but he also praised Aguero's all-round contribution – an area where he has previously suggested the Argentina international falls short.
"He played good, real good. He fought and he scored a goal. His confidence, for us, is so important. I'm so happy for him," the former Barcelona boss said.
"He was important before the game and is now. It is so important, when you play in a lot of competitions like the Champions League you need all the players."
Despite City now sitting at the front of a congested chasing pack, Guardiola still feels a making a genuine challenge to Chelsea in the title race is a fanciful prospect.
"The gap is still so long. You expect that they are going to lose games, but it is so, so difficult [for City] to win all the games," he said, having been impressed by Antonio Conte's men in their 1-1 draw at Burnley on Monday morning (AEDT).
"The gap is too big. Yesterday they didn't win but they played so solid. It is so difficult to create chances against them.
"We must focus game by game and improve our performances. My feeling is that in the last games our performances are much, much, much better.
"The only regret is we created so many chances and did not score more but I am so, so happy for the performance."
Jesus was not the only casualty of a pulsating contest on England's south coast, with Bournemouth captain Simon Francis and on-loan Arsenal midfelder Jack Wilshere also making way before the interval.
"We were hampered by our injuries in the first half," manager Eddie Howe said.
"Losing both players was a real blow. We reorganised and had a go but ultimately they were too good.
"Simon felt his hamstring and Jack had a pain in his ankle. Hopefully nothing serious."