The proposal was initially vetoed last month as clubs in League One and Two were unhappy about the disparity between the payments they received and those given to Championship clubs.
Parachute payments made to clubs relegated to the Championship have been extended, they will now receive £12m a season for four seasons rather than £16m over two years.
"Following a frank but constructive meeting at Walsall's Banks's Stadium, Football League clubs have voted to accept the Premier League's revised solidarity and parachute payments proposals," read a statement from the Football League.
"Whilst many clubs expressed concerns about the proposals, their acceptance was considered the only viable way forward. The Football League will work in good faith, with the Premier League to ensure that the resulting contract and regulatory changes are good for both competitions and football as a whole."
Championship clubs who are not receiving parachute payments will now get £2.2m a year, up from £830,000. The Premier League can afford the payments due to a record overseas TV rights deal.
League One clubs will now receive £325,000 rather than £108,000 with League Two sides gaining £250,000 rather than £72,000. Greg Clarke, chairman of the Football League, felt the outcome was best for the 72 clubs.
"This is not a perfect deal, this is a deal that, in the round, is the right thing for the Football League to do," he told the BBC.
"We stuck to our position, we got some reasonable compromises agreed with the Premier League and I think this a deal that works for both parties so I don't feel in any way hard-done by."
There were fears Championship clubs would seek to breakaway and form a second Premier League if it was not accepted. Clubs in the lower two divisions fear it will effectively create a second tier "by stealth" anyway.