Stones has yet to play for City this season due to a hip injury and Silva has missed the last two league games.
"They feel better. Bernardo better than John. Both travel and we decide tomorrow," Guardiola told reporters.
"Really happy they are back. John has not played one minute this season, Bernardo had an injury and the birth of his beautiful baby daughter but they're back and it's good news for us."
City won the Champions League for the first time last season, and defeated Leipzig along the way. A 1-1 draw away was followed by a 7-0 thrashing in the home leg, but Guardiola is not taking anything for granted.
"It's another game, another competition. It was a really good game for us, we had an incredible run at home, we had a feeling in our bones, we wanted to make the final again and we did it.
"Now it's the group stage, it's completely different. They are doing really good things, how they attack the space... it's a huge step for us if we get a result to get to the next round."
Guardiola's side appeared to be unstoppable when they won their first six league games of the season, but they have now lost two in a row. After losing to Newcastle United in the League Cup, they were beaten by Wolverhampton Wanderers in the league last weekend.
"I don't know what's going to happen this season. What the players have done is unbelievable. We concede two shots on target and we lost the game, that's football," said the Spaniard.
"We have to improve yeah, the base of what we did last season was Stones, Rodri, Bernardo, (Kevin) De Bruyne, (Ilkay) Gundogan, (Jack) Grealish and they weren't there.
"Sometimes you have to adjust something, it's normal. We're not going to win the Premier League at Wolves or lose it. We've been behind many times."
Rodri missed those recent defeats through suspension, but will now be available for the Champions League game.
"Rodri is going to play the game and after that he is going to take a rest, go to Madrid for five days before joining the national team."
Manchester City travel to Germany later than expected on Tuesday, after their flight was delayed, and will face RB Leipzig on Wednesday in Group G of the Champions League.
Both sides have three points having played one game each.
