The new structure will be in place in time for the start of the 2013-14 season and brings an end to fears that Division One clubs could break away.
The structure of the league - with 12 sides in the top flight and 10 in each of the lower divisions - is the same as the earlier plans, although clubs in the second tier will receive more money after it was revised.
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SFL chief executive David Longmuir said: "I feel there were some reluctant heroes today. We have always embraced the big principles but once you go behind the big principles like governance, distribution and one league body, there were areas of major concerns.
"But nevertheless a lot of them have seen it for the good of the game and we all accept that Scottish football is better governed under one roof.
"On June 27 there will be a formalised completion of the process and the first board meeting of the new organisation - the SPFL - will take place that day and at that point a board will be appointed."
While president of the SFL, Jim Ballantyne, added: "We are joining their company, their organisation. They have swallowed us up. We could use nice words about it, but it is a takeover.
"It is very sad that the Scottish Football League has had to be a casualty but unfortunately we were left with one option.
"Did I want to see the end of the Scottish Football League? Absolutely not. Did I want to see football strive forward? Then yes. It will be for others to decide if this step takes us to where we want to go."