The antique was expected to fetch at least a four-figure sum during an online auction on Tuesday.
Dr Anna Groundwater, principal curator of renaissance and early modern history at National Museums Scotland, welcomed the purchase.
This object has not been seen in public since 1901, so we’re very pleased to bring it into the National Collection
Dr Anna Groundwater
She said: “This is an important addition to our collection and we are delighted to have saved it for the nation.
“It has a direct connection to the Royal Stewart dynasty and moreover shows how King James V was prepared to give status and financial security to his illegitimate offspring, whilst also protecting his regional interests.
“This object has not been seen in public since 1901, so we’re very pleased to bring it into the National Collection where we will be able to put it on display in due course.”
The seal – which relates to Melrose Abbey – had been displayed during the Glasgow International Exhibition at Kelvingrove Park which attracted more than 11.5 million visitors.
Since then the seal has been in private ownership, but it will now be added to the organisation’s Scottish History and Archaeology collections.