Fifa had initially limited the number after president Sepp Blatter criticised mass changes in international friendlies. The ruling was passed at a Fifa meeting and began on July 1.
But the rule caused the Fulham-Watford friendly on Saturday to be abandoned at half-time with the referee walking out after the teams put on 27 replacements.
The game was eventually completed as an exhibition match with a linesman taking over as referee, but the FA was suitably concerned to take the matter up with the game's governing body.
After two days of negotiations, the FA has managed to persuade Fifa president Blatter that unlimited substitutions are an essential component of any pre-season campaign.
The Whites have their first pre-season friendly against Bodens BK (Sweden) tomorrow.