The Bull of Foundation is one of a series of six letters from the Pope, sent in 1413, which brought the institution into existence.
It took experts three weeks to restore the Papal Bull, including surface cleaning, repairing edge tears and the realignment of the document's silk tag.
The document will now be able to be displayed to the public.
Experts from the University of Dundee's Book and Paper Conservation Studio worked on the document. The work cost £600.
Rachel Hart of the University of St Andrews said: "We are the custodians of a vital piece of evidence not only of the university's history but also of its place as an international seat of learning within the history of Scotland.
"The Bull of Foundation is an amazing document to see and I hope that with the 600th anniversary approaching, many may have the opportunity."
A school of higher studies was started in May 1410 in St Andrews before the "third oldest university in the English speaking world" was formally founded, a spokeswoman said.
The Bull of Foundation recognised the school as a properly constituted institution.
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SIC: BBC