Chef-owner Massimo Bottura was presented with the award at a star-studded ceremony in New York last night (13 June).
The restaurant – famous for its avant-garde take on classical Italian dishes – knocked the Roca brothers of El Celler de Can Roca in Spain off the top spot in to second place after being beaten in 2015.
Danish restaurant Noma, a four-time winner which dominated the list in 2010-14, slipped to fifth behind New York’s Eleven Madison Park (3rd) and Peruvian restaurant Central (4th).
It was a mixed night for the UK, with the number of London restaurants on the list increasing from two to three.
Shoreditch’s The Clove Club was the highest new entry at 26th while Notting Hill’s The Ledbury rose to 14th, but Dinner by Heston Blumenthal in Knightsbridge fell from seventh to 45th place.
The awards also recognised some of the individuals behind the world’s top restaurants.
Joan Roca, of El Celler de Can Roca, received the Chef’s Choice award, while ‘Picasso of pastry’ Pierre Herme won the World’s Best Pastry Chef.
Dominique Crenn of San Francisco’s Atelier Crenn was named the World’s Best Female Chef, while Alain Passard - whose Paris restaurant L'Arpège was ranked 19th in the list - received the Lifetime Achievement Award.
William Drew, group editor of The World’s 50 Best Restaurants, said: “It has been a hugely exciting year with the launch of the global tour and our first awards event in New York. It is fantastic to have such a variety of culinary talent celebrated here tonight. As the appetite for reaching new gastronomic heights continues to grow we feel privileged to play a part in this journey of discovery and are proud to bring together this unique community of extraordinary visionaries within the industry.”
The World’s 50 Best list is voted for by almost 1,000 leading chefs, restaurateurs, food writers and critics across the world based on their restaurant experiences over the last 18 months.
Next year’s awards are set to take place in Australia for the first time. Just one restaurant Down Under features in this year’s top 50 list - Attica in Melbourne at 33.
The full list of The World’s 50 Best Restaurants 2016:
To view this year’s 51-100 list click here.
For 2015’s Top 50 list click here.