The rookie rule was implemented as part of MotoGP's 2010 cost-cutting push, and was aimed to spread talent around the satellite teams.
Moto2 championship leader Marquez has been strongly linked to a factory Honda seat next season after Casey Stoner's decision to retire, but had the rookie rule stayed in place, it would have been necessary to place him at a satellite team for a year first.
The commission also approved a limit of four bikes - two works and two independent - per MotoGP manufacturer in 2013.
It rejected moves to ban spare bikes and non-ferrous brake disc material, both of which had been proposed as cost-saving measures.
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