The 1996 cartridge was a launch title for the Nintendo 64 console, and was one of the most influential early 3D platformers.
The auction house said there were "fewer than five" copies in such good condition.
The sale dwarfed another record-breaker, an original Legend of Zelda cartridge, set just two days before.
That original Nintendo Entertainment System (NES) cartridge sold for $870,000 on Friday, briefly making it the world's most expensive game.
Neither game was bought for the rarity of its gameplay experience - Nintendo has rereleased both for its Nintendo Switch console.