The boss expects Stones to be out for several weeks with the hamstring injury which forced him off at the weekend, though there is better news for Silva, with Guardiola suggesting he has been left at home as a precaution.
The duo join Sergio Aguero on the sidelines and Guardiola admitted it remains unclear as to when the Argentine will be ready to return from the muscle injury he suffered against Chelsea last month.
READ | Which TV channel is Dinamo Zagreb v City on?
“David had a huge kick in the dangerous part of his leg and it was too much of a risk to play,” said Guardiola on Tuesday evening.
“John is injured for a few weeks. Sergio is much better, but is still not ready. I don’t know [how long he will be out].”
Stones‘ injury leaves Guardiola with just one senior centre-half in the form of Nicolas Otamendi, but Guardiola continues to see Fernandinho as a viable defensive option in Aymeric Laporte‘s absence.
Teenagers Eric Garcia and Taylor Harwood-Bellis were included in the travelling party to Croatia, with Guardiola suggesting the former may be afforded first team opportunities whilst Stones is sidelined.
“Yeah,” he added when asked if the Spaniard has a chance to play. “We have two and Eric. Of course, Rodri can play there.”
Whether either of the youngsters will feature against Dinamo remains to be seen.
With City having already qualified for the Champions League last 16, the Catalan says he will take advantage of the opportunity to rest players ahead of the busy festive Premier League schedule, but remains committed to naming a strong side that will aim to complete the group stage in positive fashion.
“We have the two young players,” Guardiola explained.
“We have many injuries. The rest of the squad is here. We are going to put out the best squad in the circumstances.
“Of course, we have already qualified and the Premier League is more important right now than the Champions League.
“We are going to make some changes, but we have a good squad to try to compete and to get a good result.”