The SRU had warned that funding problems could force them to scrap one of its Celtic League sides.
But a private company, headed by businessmen Alex and Bob Carruthers, has agreed to finance Edinburgh for the next five years, ensuring the future of Glasgow Warriors and Border Reivers as well as Scotland's capital club.
SRU chief executive Gordon McKie said: "This is an important development for all of us at Scottish Rugby and one we are determined to see succeed.
"This is a considerable commitment by our new partners and we look forward to working closely and effectively with them.
"It confirms our belief that the Scottish Rugby brand continues to move from strength to strength."
The Carruthers management team will take charge of the Edinburgh pro team, who will continue to play their home games at Murrayfield for the foreseeable future, and its staff ahead of the new season.
The SRU will have a place on the new company's board and will continue to provide funding and support to the new owners in development, with the right to call up Edinburgh players and coaches for national squad and representative
McKie added: "Scottish Rugby is committed to controlling the debt situation and this is exactly the sort of pro team business model we wanted to work towards.
"By the start of the new season the Edinburgh team will be run by new owners, backed by Scottish Rugby."
Former Scotland Under-21 and Caledonian Reds player Alex Carruthers will be executive chairman of the new company.
Ten weeks ago Scottish Rugby announced it would seek to enter joint venture partnerships with external investors for one or more of its three professional teams, in an effort to stem the governing body's core debt of more than Â£23million.
Bob Carruthers, who will be the principal shareholder in the new agreement, said: "Alex and I are hugely excited by our new partnership with Scottish Rugby.
"We are rugby fans through and through and to take over the running of the Edinburgh team is very special.
"The sport has much to offer and we see tremendous scope to develop mutually beneficial plans here at Murrayfield."