The flamboyant 42-year-old, who was born in Nagano, was the biggest winner on a night when Japanese cooks triumphed in the backyard of French haute cuisine.
Kazuyuki Tanaka won two stars for Racine, his restaurant in the northeastern city of Reims, as did Yasunari Okazaki for his sushi and crossover cuisine at L’Abysee au Pavillon Ledoyen in Paris.
Kobayashi — a striking figure with bleached blond hair — said Japanese cooks have earned their place at the top table of French cuisine.
“There are lots of Japanese chefs now in France and you have accepted us and given us a place,” he said as picked up the highest distinction in French cooking.
“Thank you, France,” he added.
Kobayashi admitted that his perfectionism can make him a “difficult person” to work with.
“I am quite hard. I ask a lot of my team, and then I ask a lot more,” he joked.
A dozen top Japanese cooks in France have shaken up the elite ranks of the Michelin in recent years, led by two-star chefs Takao Takano in Lyon and Masafumi Hamano at the Au 14 Fevrier near Macon in rural Burgundy.
Last year, Keigo Kimura at the Asperule in Dijon and Takafumi Kikuchi at La Sommeliere in Lyon won their first stars for helping to re-define and re-invent French cuisine.
Kobayashi opened his restaurant, Kei, in centre of the French capital nine years ago, and wowed diners with such dishes as sea bass cooked on its scales and smoked salmon with roquette mousse and a tomato vinaigrette with lemon emulsion.