Parking his car at the end of the pitlane, in the wrong place, the Briton stood up in jubilation and then jogged back to the garages waving at the fans in the packed grandstand opposite.
In seven years as a Honda driver, the 31-year-old with a deep love of the country and a Japanese girlfriend had only once managed to appear on the podium at the Honda-owned circuit.
This year's race was made more emotionally-charged by Button's involvement in fundraising efforts to help victims of the earthquake and tsunami that devastated a swathe of northeast Japan earlier this March.
"It feels like a home win, and it's a very emotional win, not just for myself, but the whole team, and especially my close-knit little team of (trainer) Mikey (Collier), the old man (father John) and (girlfriend) Jessica (Michibata)," the 2009 world champion told Reuters.
"Obviously that's because of the connection with Japan through Jessica, who was bawling her eyes out after the race, so it was very difficult for me to stop myself from crying.
"But it was a very special race for all of us, and also because this circuit is just phenomenal, a work of art I would say," added the Briton.