Joubert had led after Wednesday's short programme and was a class above his rivals again with a flawless routine that brought the Tokyo crowd to his feet and left the Frenchman in tears.
"I worked hard for this gold," said Joubert, who posted a winning total of 240.85 points. "It's been a great season. I gave it everything I had. But waiting for the scores was torture."
Japan's Daisuke Takahashi also broke down after taking the silver with a total of 237.95 while two-times defending champion Stephane Lambiel of Switzerland was third with 233.35.
Czech Tomas Verner was fourth with 226.25 with American Evan Lysacek fifth on 222.18.
Canadian champion Jeffrey Buttle, second after Wednesday's short programme, blew his chances by crashing to the ice three times in an unhappy skate and finished sixth on 214.96.
Sweden's Kristoffer Berntsson brought some Travolta-esque dazzle to Tokyo with a rousing skate to the music from "Saturday Night Fever" which briefly gave him the lead.
The Nordic champion eventually finished ninth on 206.29 points despite bringing the house down with his high-intensity routine.
Russian three-times world champion Yevgeny Plushenko is on a year's sabbatical following his gold medal at last year's Turin Olympics.