The model will also see a Port Adelaide academy side consisting of players aged between 18 and 22 play in the SANFL reserves competition.
All non-selected AFL players will line up for the Magpies in the SANFL competition and wear the club's traditional black-and-white, 'prison bar' jumper.
A group of 15 'top-up' players will be contracted to play only at SANFL level to complete the Magpies team.
CEO Keith Thomas said in a statement on Tuesday night that Port Adelaide was now truly united.
“We are now, finally, one club, and all of Port Adelaide’s players will exclusively play for Port Adelaide,” Thomas said.
“This important decision allows us to field teams committed to excellence in the AFL and SANFL as a united club."
The Power had looked as though they would be the only AFL team to be without a seconds side in 2014 after the Crows accepted the SANFL's invitation to join it earlier in the year.
The major flaw in the SANFL proposal was the abolishment of Port's junior structure.
Thomas had previously stated the club's tie to its community was paramount in its future plans.
Although he agreed to the model that will see the disbandment of the club's junior structures as it knows them, they will be replaced with alternative options from the start of 2015.
Instead of fielding teams in the under-18, under-16, under-15, under-14 and under-13 competitions, the club has promised to implement a range of development programs aimed at junior footballers.
As well as metro and country programs, the club will run indigenous, international and father/son programs.
Thomas said such initiatives would satisfy the club's desire to remain in touch with its community.
“One non-negotiable was that we must be able to maintain our commitment to both elite and grassroots football in South Australia," he said.
"We are delighted to have achieved this through this proposal.
“I thank all of the key stakeholders who have helped achieve this outcome and extend particular thanks to our supporters who have been very understanding of the situation we have worked through over the last three to four months.”
Twitter: @AFL_Harry
