The glass, engraved with two verses of the Jacobite anthem, went under the hammer at Halls fine art auction house in Shrewsbury.
Halls said the glass was one of a number in the auction celebrating the movement that plotted against Protestant kings of the 17th and 18th Centuries.
The bids quickly exceeded pre-sales estimates of £20,000-£30,000, it added.
The glass was bought by a telephone bidder from London. Halls said it is among fewer than 40 known examples in the world.
The collection containing the Lennoxlove Amen glass had belonged to the late Edward V. Phillips, who was a corn merchant.
Amen glasses were passed around in secret societies devoted to the restoration of a Catholic monarch, the auctioneers said.
Jeremy Lamond, Halls’ fine art director, said: “These glasses are testament to the fact that this was perhaps one of the few times in the history of alcohol when the glass was more dangerous to the imbiber than its contents.
“For those caught with such articles, penalties were severe, including imprisonment and, sometimes, execution.”