The Toffees retain a long-term lease on the facility but will now pay reduced
annual costs to the council instead of a private company.
The arrangement should ease some of the pressure on the club's finances but it is also expected to be a money-spinner for the local authority, whose loan for the purchase could be paid off in just 25 years, it is understood.
"We continue to work with the council on many fronts and the club is especially pleased to have delivered an innovative scheme, on our superb Finch Farm facility, that works for both parties," said Everton chief executive Robert Elstone.
Mayor of Liverpool Joe Anderson added: "It's a very good deal for us and for Everton.
"Over the lifetime of this arrangement we will get much-needed revenue, which we can re-invest in essential services for the people of Liverpool.
"Together with the new Exhibition Centre, the council regard such investments as innovative but vital in enabling it to meet its on-going budget challenges."