The US motorbike maker gave the 1,585cc Dyna Super Glide to the pope in June to mark the brand's 110th anniversary, and while the 77-year-old never rode it, he signed it before donating it to Roman Catholic charity Caritas Roma.
"It's a record for a post-vintage motorbike, from the 21st century," said Bonhams France, the auction house, adding the bike was purchased by an unidentified European buyer.
The funds from the sale will go towards the restoration of the charity's hostel and soup kitchen based at Rome's Termini railway station.
A jacket that was also given to the pope by Harley-Davidson was snapped up for €57,500.
The bike is on show at the Grand Palais in Paris - where the auction took place - among hundreds of other iconic vehicles such as Rolls-Royces and Cadillacs.
According to Bonhams, Pope Francis has another Harley-Davidson, although the famously humble pontiff is more of a fan of buses.
He opted to ride one the day after his election last year instead of taking a limousine, and regularly used them in his homeland Argentina instead of taxis.