Mark Palios, the FA's Chief Executive, said: "I am delighted that FIFA have listened to our concerns and clarified the situation.
"Unrestricted substitutions in pre-season friendlies are in the interests of clubs and players alike, and allow proper preparation for the coming season."
City's pre-season schedule had been under threat if a change wasn't made. Peter Taylor went ahead with last night's friendly at Bishop's Stortford and made only six substituions, but this resulted in City playing out the last 20 minutes with only 10 men after Andy Dawson suffered a slight hamstring strain. Taylor is now set to field different sets of 11 in each half of Friday's game at Canvey Island follow the laxing of the rules.