The 'solidarity package', the biggest major investment handed to Football League clubs as a body since the ill-fated ITV Digital deal, ensures a proportion of top-flight income is redistributed down the professional football pyramid.
The money - £31.8million next season - is to be split among clubs but portions of it must be spent on youth development and community programmes.
With the Premier League set for a cash windfall of £2.7billion from their new television deals over the next three seasons - up more than 75% on the previous three years - the funding could be regarded as little more than small change.
But Football League chairman Mawhinney insisted the Premier League should be praised for their contribution.
He said: "This is a generous gesture by the Premier League and, on behalf of our clubs, I offer my thanks.
"In part, the need for a payment of this kind stems from the significant financial gap that exists between their league and ours - largely due to the financial success of the Premier League. This positive initiative will help to address this issue."
Mawhinney's thanks were echoed by Preston chairman Derek Shaw, who sold prize asset David Nugent to Premier League Portsmouth this summer.
He told the club's official website: "It's magnificent news. It's fantastic that the Football League board have negotiated this with the Premier League and it's great for clubs like Preston North End who as we all know find it very difficult competing."
He added: "It will help us on the youth development side, we are keen to push more of our homegrown players, which for a number of years we have not had the results that we should be getting.
"We will have to try to make sure that it doesn't end up on player wages, the money is there to help the clubs survive long-term and invest properly."
Premier League chief executive Richard Scudamore said: "The Premier League and our member clubs recognise the importance of the continued health of the professional game at all levels.
"This solidarity payment means that Football League clubs will have the ability to increase investment in critical areas such as youth development and community programmes, as well as receiving an extra payment virtually equivalent to the one a Championship club receives from their own basic award."
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