They both trailed 1-0 at half-time, but Sergio Aguero's equaliser and a victor from Kyle Walker four minutes from time earned champions City a 2-1 home victory over a gritty Southampton side.
"I didn't speak with the doctor, but when he [Silva] has a muscular problem and can not play more minutes it is because he has something, and when it is a muscular problem it is always a minimum of 10-12 days", Guardiola said.
"We will try to win, but if not, there is Shakhtar at home and Dinamo Zagreb away".
"We're going to play with the best team possible to win at Atalanta and after we go to Anfield".
"No comment on that", Guardiola added.
"The first half was very even, up until 3-1".
"It's a tight turnaround, but we'll prepare as best we can". "We are disappointed but when you come to places like this you have to take control of the game", Solskjaer said.
For City, the hero was Kyle Walker, setting up one goal and scoring the victor against Southampton in the 86th minute.
"We've earned to the right to play such opponents", said Toloi.
"Now we go to Italy and when we come back we go to Anfield. We know that with our fans at home we can do well".
Duván Zapata still remains absent for Atalanta with an abductor injury.
When does Atalanta vs Man City kick off? .
Key stat: No one has created more goals in the Champions League for Man City than Riyad Mahrez (3).
"I think they believed in themselves and that they were challenging, but did they honestly believe that they would go on and win it?"
"We look at ourselves, we know which team we face, I think they have won 10 and drawn one".
Pierluigi Gollini has conceded more goals than any other goalkeeper in this season's Champions League (11) - the last goalkeeper to concede more in their opening three appearances in the competition was Legia Warsaw's Arkadiusz Malarz, in October 2016 (13).
A win in Atalanta will secure a spot in the Champions League last 16 for Pep Guardiola's men with two matches to spare.
Their five goals against Atalanta were split between Sergio Aguero and Raheem Sterling.
City's three victories have put them five points clear at the top of Group C and another win here would see them qualify with two games to spare.