The new Celia Sinclair Charitable Trust has acquired the Category-A listed building for about £400,000. The building, which needs about £900,000 of further repairs, will be gifted to the city by the Trust.
The Mackintosh-designed building and interiors, which were designed and built in 1903 for Kate Cranston, are situated in Sauchiehall Street. The Willow Tea Rooms opened in November 1904 with the Room de Luxe as its main attraction, featuring silver furniture and leaded mirror friezes.
Mackintosh had complete control over every design in the property, including the cutlery and waitress dresses.
Ms Sinclair said: "The Willow Tea Rooms is an iconic building and I couldn't simply stand by and watch it deteriorate. I'm a proud Glaswegian and I want to see its heritage preserved for the generations to come.
"I started this project over a year ago. The recent tragic fire at the Glasgow School of Art has underlined to me, and others, that we really do need to act to safeguard what remains of Mackintosh's work.
"The Trust will ensure that after the renovation work the building will be financially secure and that due care and attention will be given to the building forever."
Work to make the building wind and watertight will require a minimum investment of more than £400,000.
In addition, the restoration work on features lost of damaged will cost at least another £500,000.
Anne Mulhern, who has run the Willow Tea Rooms restaurant since 1983, said: "After years of uncertainty I am relieved that we now have ownership back in Glasgow with someone who obviously cares about the building and will make sure that Mackintosh remains open for business in the city."
Work on revamping the building is due to get underway next year.
Its name comes from Sauchiehall Street, on which it is situated, which in Gaelic means "alley of the willows".
A leading Mackintosh expert, Roger Billcliffe, has agreed to join the board of the new charitable trust.
He said: "I am delighted to be joining the board as I believe that there is so much we need to protect and recover and Celia has the drive to make it happen."