The 28-year-old missed the 4-0 win away against Sevilla last week due to a minor muscle problem, but he has since returned to first-team training and will be in contention to face BVB at the Etihad Stadium.
Aymeric Laporte was also spotted in training and completed his first session with his teammates after undergoing knee surgery over the summer.
The Frenchman is unlikely to feature in Wednesday’s matchday squad, however, while Kyle Walker is ruled out as he continues to recover from a muscle injury.
The England right-back came off in the final 10 minutes of City’s Premier League draw at Aston Villa and subsequently missed the victory over Sevilla.
Speaking at a press conference on Tuesday, Guardiola provided an update on all three defenders, telling reporters: “John [Stones] is training, Kyle [Walker] doesn’t. John is fit and good.”
“It is the first training session [for Laporte] and I don’t know, but this is good. It is going really well and we are very happy for that. After the international break he will be ready for us to think about using him.”
When asked whether Laporte could be named on the substitutes’ bench on Wednesday, Guardiola added: “I don’t think so, but we will see. Training session yesterday was partial, today complete.
“I spoke with the doctor, he needs a little more volume on his leg but in general he’s going well.”
The rest of Guardiola’s squad is fit and available for selection on Wednesday, including former Borussia Dortmund trio Ilkay Gundogan, Erling Braut Haaland and Manuel Akanji.
Guardiola believes the German outfit could use their knowledge of all three players to benefit when they face City both home and away in Group G.
“[Dortmund] know these players (Gundogan, Haaland and Akanji) more than I know Dortmund players, that is for sure,” said the Spaniard.
“They were there a few years. They can benefit. We will see tomorrow if it is an advantage. But also, they know the Dortmund players, too.”
Since losing to Liverpool in the Community Shield, Man City have put together a seven-game unbeaten run across all competitions this term, scoring 23 goals – including 12 strikes from Haaland – and conceding only six.
Dortmund, meanwhile, won their opening two games in September against Hoffenheim and Copenhagen, but they head into Wednesday’s encounter off the back of a disappointing 3-0 Bundesliga away defeat to RB Leipzig last weekend.