The pair have often competed at the annual July 4 hot dog eating championship on Coney Island, New York, with Chestnut winning last year's title with a five-dog eat-off after they were tied with 59 franks in ten minutes.
However, Kobayashi gained revenge by eating five-and-three-quarter P'zones - a cross between a pizza and a calzone - in six minutes, while Chestnut could only manage five-and-a-half, The AP reports.
Chestnut said: "I'm a little bummed. There's nobody I like beating more than him, he pushes me harder than anybody.
"It was tough. Kobayashi came to win. I was raised on pizza so it was natural for me to eat it, but I was a little slow to get going and he came out fast."
Kobayashi said: "I love pizza. When I come to America, pizza is my happiness. I look forward to eating it.
"I wanted to prove that I'm champion. A champion will stand up to any battle."