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Referee Andre Marriner retrieved several coins that were thrown towards City striker David Faupala and his team-mates as they celebrated his equaliser.
Manchester City went on to lose 5-1.
"We condemn such idiotic and dangerous behaviour," a Chelsea spokesman said.
"It is also worth stating this is a criminal offence and we will support any police prosecution if they can be identified."
The incident came a day after West Bromwich Albion's Chris Brunt was struck just beneath the eye by a coin as he went to throw his shirt into the visiting fans after their defeat at Reading.
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Describing the incident at Stamford Bridge, Chelsea manager Guus Hiddink added: "I saw it and I condemn it strongly and I think Chelsea will react. These people must not come into the stadium."
Hiddink, meanwhile, insisted the traditions of the FA Cup must be protected after City played five teenage full debutants in their side ahead of their Champions League last 16 game against Dynamo Kiev in Ukraine on Wednesday.
He said: "Many people worldwide are focused on the FA Cup. As a youngster I knew which Saturday was the FA Cup.
"It is the temple of football worldwide and we must be careful not to devaluate it."
Chelsea will impose life bans on supporters who threw coins at Manchester City players during the FA Cup fifth-round tie at Stamford Bridge if they can be identified.