The controversial 'Super 8' format, which has been rejected by the two players organisations, was passed with 76% of the vote.
The structure sees counties split into two groups of four with the top two qualifying for the All-Ireland semi-finals.
It will be in place for a three year trial period from 2018.
Also at Congress, delegates have voted to move the All-Ireland hurling and football finals to August instead of the traditional September period.
And another new rule will see extra-time in all hurling and football championship games, except provincial and All-Ireland finals.
