The watch was sold for a premium inclusive £4m (CHF5.06m).
Following an eight minute bidding war, between ten bidders in the room and three on the telephone, the winning bid for the Reference 6062 watch was from an unnamed bidder on the phone.
The sale at Phillips, in association with Bacs & Russo, was part of a two day auction at Hôtel La Réserve in Geneva.
Aurel Bacs, senior consultant, said: “Phillips has now surpassed its own world auction record for a Rolex, set in this saleroom 12 months ago. The combination of the iconic name Rolex, its extraordinary rarity and originality, crowned by the imperial first owner, [were all factors in making] this world auction record result."
The late emperor bought the watch during Geneva peace negotiations in 1954. It was first sold at auction in 2002 at Phillips.
He said the watch, with a triple calendar and moonphase in yellow gold, is considered by the collecting community as being amongst the most valuable and desirable Rolexes ever made.
It is one of only three black dial models with diamond markers, and thought to be the only one with diamond markers at the even hours.