After lobbying from the FAI, FIFA have changed the rule to accommodate countries which run a summer programme, allowing players to transfer and line-out for a third club if that club plays summer football.
Gareth Farrelly and Colin Healy where unable to play for Cork City until July of last year due to this rule.
The rule, which operates from July 1 to June 30, did not facilitate countries whose season was during the summer, but FIFA have now amended it.
The new rule states: 'Players may be registered with a maximum of three clubs during one season. During this period, the player is only eligible to play official matches for two clubs.
'As an exception to this rule, a player moving between two clubs belonging to associations with overlapping seasons (i.e. start of the season in summer/autumn as opposed to winter/spring) may be eligible to play in official matches for a third club during the relevant season provided he has fully complied with his contractual obligations towards his previous clubs.'
Eircom League of Ireland Director Fran Gavin said: 'We took the decision to point it out to FIFA because we were not prepared to run the risk of receiving sanctions for breaching it.
'The change will greatly benefit the eircom League of Ireland and the players in it.'