Bocuse, who came from a dynasty of cooks going back to the 18th century, died in his sleep in the room in which he was born on Saturday.
He had been suffering from Parkinson's Disease for several years.
Service continued as usual at his flagship restaurant, the Auberge de Collonges on Saturday.
Bocuse inherited the restaurant from his father, Georges, having worked there with him and won his first Michelin star for traditional regional cooking that was simpler than the sophisticated cuisine he would later develop.
His paternal grandfather had run the Restaurant Bocuse at Collonges while his mother's parents ran the Hôtel du Pont, 400 metres away.
Georges Bocuse bought out his in-laws' partners and changed the hotel's name to the Auberge du Pont.
Paul would later buy back his grandfather's restaurant, which had slipped out of the family's control, and restore its old name.
Chicken, pig's bladders, crayfish, truffles
Paul Bocuse left an indelible mark on French cuisine, partly thanks to the praise of the world-famous Gault-Millau Magazine.
In the 1970s its editors, Henri Gault and Christian Millau, announced the arrival of a "nouvelle cuisine" in France, hailing Bocuse as one of its initiators, although the movement was to become identified with a more austere style than his.
Among his specialities were gratin of crayfish tails, poularde (fattened chicken) cooked in a pig's bladder and a black truffle soup, which he named after Valérie Giscard d'Estaing, the president who awarded him France's highest honour, the Légion d'honneur.
Businessman and ambassador for French gastronomy
As well as being a creative chef, Bocuse was a champion of French gastronomy and an aggressive businessman, building an restaurant empire first in France and then around the world, as well as reaping profits from spinoffs in his name and several books.
He also had an enormous appetite for life, having nearly died when fighting with General de Gaulle's liberation army at the end of World War II.
He was saved by American soldiers, who donated blood and tattooed a French cockerel on his shoulder and adopted the motto, "Work as if you are going to live 100 years, live as if you are going to die tomorrow."
In a book published in 2005, Paul Bocuse, le feu sacré, he admitted to being "polygamous", having married his wife Raymonde, with whom he had a daughter, in 1947, had a son with former clinic manager Raymone Carlut, and enjoyed a relationship with his press attachée, Patricia Zizza, whom he met in the 1970s.
"Monsieur Paul, that was France. Simplicity & generosity, Excellence & art de vivre. The gastronomes' pope has left us. let our chefs, in Lyon as in the four corners of the world, cultivate the fruits of his passion for many years," Collomb said in a Twitter tribute.
Paul Bocuse, a life in dates
- 11 February 1926: Born in Collonges to restaurateurs Georges Bocuse and Irma, née Roulier;
- 1936: Parents take over maternal grandparents' hotel, changing it to the Auberge du Pont;
- 1941: Starts work at Claude Maret's La Solerie restaurant in Lyon;
- 1944: Joins General Charles de Gaulle's liberation armuy, wounded in Alsace, saved by American soldiers;
- 1946: Employed by Eugène Brazier at the Col de la Luère near Lyon;
- 1946: Marries Raymonde Duvent:
- 1947: Daughter Françoise born;
- 1940s and 50s: Works in varioius restaurants in Paris and other cities;
- 1958: Returns to work at family restaurant in Collonges, awarded first Michelin star with his father;
- 1959: Father dies:
- 1961: Wins Meilleur Ouvrier de France competition;
- 1962: Second Michelin star for l'Auberge Guingette;
- 1965: Third Michelin star;
- 1969: Son Jérôme born;
- 1970: Establishes the Société de la Grande Cuisine Française with Christian Millau, Henri Gault and 12 Michelin-starred French chefs;
- 1975: Awarded Légion d'honneur by President Valérie Giscard d'Estaing;
- 1982: In partnership with Gaston Lenôtre and Roger Vergé takes over management of the Pavillon de France at Disneyworld, Florida;
- 1987: Establishes the Bocuse d'Or world cookery championship:
- 1990: Establishes the Paul Bocuse Institute chefs' school;
- 1991: First chef to be represented as a waxwork in Paris's Musée Grevin;
- 2004: Established the Paul Bocuse Foundation to train chefs, made a Commandeur de la Légion d'honneur by President Jacques Chirac;
- 2007: Opens first restaurant in Japan;
- 2011: Named Chef of the Century by the Culinary Institute of America;
- 2015: Jérôme Bocuse takes over running of Lyon brasseries;
- 20 January 2018: Dies at his restaurant in Collonges.