The Rosemere, Que., freestyler won the final race of the season by taking the dual moguls competition while his teammate Mikael Kingsbury of Deux-Montagnes, Que., came second but took his third straight World Cup title on Friday.
"It's been an amazing ride," said Bilodeau. "Very emotional."
The two-time Olympic champion had no chance to catch Kingsbury for the Crystal Globe as overall champion, but wanted to push his friend and rival to the limit in the last race of his career.
Kingsbury got down the hill quicker, but the judges gave the gold medal to Bilodeau on execution.
"I knew the grand prix was done and I couldn't go up or down," said Bilodeau. "I looked at Mikael and said 'I'm really honoured to have my last run against the best in the world.'
"I said 'I'll just enjoy it.' I decided to do a back double, which is something you don't do in duals. It's too risky. But I thought 'it's my last race, I'm going to go for it.' "
On the women's side, Hannah Kearney of the United States won a fourth straight Crystal Globe and the fifth of her career.
Kearney defeated Canada's Chloe Dufour-Lapointe in the final. Her sister Justine Dufour-Lapointe had a shot at catching the American for the title, but crashed in the round of 16 and lost to Perrine Laffont of France.
With his win, Bilodeau broke freestyle legend Jean-Luc Brassard's record for World Cup podium finishes with his 48th, including 19 wins.
"I never looked at the number of podiums," he said. "For me it was a day-to-day process of trying to be the best in the world.
"Records are made to be broken. I'm sure it won't last long. Mikael will break it in a year or two."
The 26-year-old, who this year became the first freestyler to defend an Olympic gold medal, now plans to finish his accounting studies at Concordia University and enter the corporate world.
Kingsbury, who has 38 World Cup podium finishes, said it was an emotional day for both skiers as they waited at the top of the final run of the season.
"We did a big hug," said 21-year-old Kingsbury. "I told him it was an honour to be at his last run.
"Then we both made amazing runs."
While Bilodeau is bowing out, Kingsbury said his career is just getting started and he intends to try to stay on top through the next Winter Olympics in 2018 in South Korea.
"I'm still young and I've got a lot to learn in the sport," he said. "I've had an amazing career so far.
"I never thought I'd do as much as I've done so far, but I'll work hard, get stronger in the gym. The best is still to come."
The three Dufour-Lapointe sisters finished just behind Kearney in women's standings, with Justine second, Chloe third and Maxime fourth.