The treasured items were among historic documents and important artefacts stored in a fire-proof archive in a lower basement in the west wing - the part of the A-listed building most affected by the blaze.
Art insiders revealed that the works were kept inside a concrete, fire-proof container which survived intact.
A source said: "One of the most important thing in all of this is that Mackintosh works are safe.
"I've been told that among the things which are fine are Mackintosh papers, watercolours and drawings. This is obviously a terrific development."
As news of the saved items came to light separate plans for a salvage operation to remove millions of pounds worth of artefacts from the gutted building were last night being finalised.
It emerged yesterday that the building and its contents were fully insured despite delays caused in the installation of a new fire "suppression" system because of the discovery of asbestos.
Art school staff are poised to go into the building today to locate and mark up thousands of items to be retrieved once fire chiefs give the all-clear.
Conservators will operate a "triage" system, marking works most in need of urgent, specialist attention.
Water damaged textiles and items which would perish if they are not given immediate attention are likely to be among the artefacts to be brought out first.
It is understood the operation to remove the objects will take several days.
The fire broke out on Friday afternoon as final year students worked on completing their entries for the end of year degree show. Several people were led to safety, though no one was hurt.
The fire service has yet to confirm the cause of the blaze, which some students say started when a spark from a projector ignited a piece of foam is a basement area.
Last night a Glasgow School of Art spokeswoman said: "The main archive is in the sub-basement and it was protected from fire. As far as we are aware the main archive is intact, although until we get in we can't confirm that."
She added: "We are putting in place a salvage plan because we need to get things out of the building.."
It is not yet known how much it will cost to rebuild the building, though the spokeswoman dismissed claims of £50 million as "speculation." She was unable to say how much the building and its contents were insured for.
She said: "The building and its contents is fully insured for fire and peril. But you have to also bear in mind how much the conservation work is going to cost and other knock on costs, such as how much it will cost to rehouse the school of fine art."
School chiefs are also working on plans to enable 600 final year students to complete their work and are considering postponing the start date for the degree show, which was scheduled to begin in mid June.
Two hundred firefighters battled to bring the fire under control at the height of the incident on Friday and many continued to work at the site throughout the weekend.
The fire chief who oversaw the operation has praised the "outstanding" professionalism of his crews.
Scottish Fire and Rescue Service Assistant Chief Officer David Goodhew described how crews were sent to each floor to create a barrier and prevent the fire from spreading.
He said: "When we arrived we made a very quick decision that we were going to try put in what we call a fire break right through the middle of the building.
"While we were doing that we sent other crews towards the fire internally and externally, and effectively fought the fire from inside and from outside to stop it getting any larger.
"The professionalism of the crews was outstanding.
"Everybody, from the person operating the pumps to the person who was running out water from the hydrants to the people inside the building, we were all working to achieve one goal - to save that building."
Community Safety Minister Roseanna Cunningham, added her praise on a visit to Cowcaddens fire station yesterday.
She said: "I think everybody has recognised the extraordinarily professional job that has been done."
Both the Scottish and UK Governments have pledged funding to help restore the Mackintosh building.