The 20-year-old was a key part of City's fluid attacking unit in the first half of the campaign, scoring eight goals in 18 league appearances.
"Gabriel Jesus will be in training today...It's good news," Guardiola told reporters on Friday.
"I don't know when he'll be ready to play – the first step was to make one or two weeks of training alone – but today will be his first training for the team."
The Spanish manager remains keen to name a strong starting lineup against third-tier Wigan as his players have five days to recover from a 4-0 victory over Basel in the Champions League.
"The Basel game was a winning game, we have six days or so and until next Sunday (the League Cup final against Arsenal) we have five or six days too," Guardiola added.
"They can recover. When the distance is two or three days after we have to take a look at the condition of the team."
Wigan famously beat City in the 2013 FA Cup final before knocking them out at the quarter-final stage a year later.
Guardiola said he was wary of his opponents, who have already knocked out two Premier League clubs - Bournemouth and West Ham United - in the competition so far.
"Of course I am concerned... Bournemouth for me are one of the teams I like to watch the most in the Premier League and they were able to beat them," he said.
"I think in the FA Cup every season there are a lot of surprises. Not just this season and last season but throughout history. We are going to prepare as good as possible for this game."
(Reporting by Hardik Vyas in Bengaluru; editing by Clare Lovell)
