The 72 league clubs met in Walsall on Thursday and voted in favour of the scheme, which was backed by the Football Association and the Premier League, although it was not unanimous, with the vote being 46 to 22, with three no-shows and one abstention.
The deal will see the current Academy system scrapped in favour of each club's youth set-up being categorised on four different levels.
Category One will be the highest but to achieve this it will cost around £2.5million, must include 18-full time members of staff and there must also be residential provision.
The EPPP will also see the current tribunal system, which is used when the buying and selling club cannot agree a fee for the transfer of a player aged under 17, scrapped in favour of a fixed compensation scheme.
This will mean in principal a selling club will be paid £3,000 per year for every year of a player's development between the ages of nine and 11. The fee per year from 12 to 16 will depend on the selling club's academy status but ranges between £12,500 and £40,000.
It means that for a Category One club to sign any player Under-17 it will cost at most £100,000.
The ruling over a player not being allowed to join a club more than an hour's drive away has also been scrapped, meaning clubs can now sign any youngster from around the country.
However, clubs in Category Three and Four can no longer sign players before the age of 12.
The Premier League had threatened to withhold their current funding to the Football League's youth programme, which equates to more than £5million per season.
Football League chairman Greg Clarke confirmed to Sky Sports News that the vote had been passed.
"We had a lively debate for nearly two hours, a lot of clubs were eager to know details and finances, and categories," he said.
"We then had a vote which was strongly supported because English football - the FA, Premier League and Football League, the national game - is all behind producing better talent for our national side and this is a move forward."
Clarke admitted that the new compensation system was an issue to some clubs.
"There are two portions to this which is the Elite Player Performance Plan, which is pretty uncontentious, which has come from a lot of work from a lot of people, but embedded within it is a compensation plan which determines how much large clubs pay small clubs for youth talent of different ages and it is important that each club knew what they were signing up for."
Asked if the plan meant that youth academies would now die off in the lower leagues, he said: "We hope not, we hope Football League plans will develop and retain.
"There is always the danger under the new scheme that larger clubs will become more predatory but we hope we don't see that.
"We should not get lost in the fact that this is a major step forward we wanted more contact hours and that is what we have got with this.
"Higher quality coaching with more contact hours and better footballers, and there may be a risk of financial consequences but we have to monitor that and make sure it doesn't happen."
Clarke admits they are hopeful no clubs would now scrap their youth system, as is the fear amongst some observers.
"It certainly won't be a positive if we lost Football League clubs from the youth development sector. Our business and country's football model is about getting talent and developing it locally, and making sure it plays in the first team as quickly as possible and that is the main aim of the Football League," he said.
"There are certainly dangers and if we start losing clubs from the youth sector that is a clear sign."
He insisted that the Football League had to back the scheme.
"The Premier League have put a proposal on the table with a lot of strengths and a couple of issues we were concerned about, one of those was compensation, but there is a lot of good things about this.
"It is a consistent approach across the English game which should allow us to compete.
"I think it is a positive step as there will be more money to spend."
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