Vaultier, a five-time World Cup champion, looked comfortable in the early stages of the competition but the unpredictable nature of the sport means that no result can be guaranteed and several of his rivals crashed out in the early stages.
The format sees the top three riders from each of the eight heats advance to quarter then semi-finals, with six competitors eventually contesting the final.
Italy's Omar Visintin, ranked fourth in the world, clashed with Spain's Lucas Eguibar at top of the run during his heat and was eliminated.
Then, in a dramatic semi-final, Vaultier tangled with Austria's Alessandro Haemmerle and Sochi silver medallist Nikolay Olyunin, an Olympic Athlete from Russia.
All three hit the deck but Vaultier managed to pick himself up first and finish the race in third, qualifying for the final.
Olyunin, touted to challenge Vaultier in the final, was injured in the incident and received treatment for a lengthy period of time, delaying the start of the second semi-final.
Russian news agency TASS quoted a team source as saying Olyunin suffered a broken leg. Australian pair Alex Pullin and Hughes also qualified from the first semi-final.
EVERYTHING TO LOSE
After more drama in the second semi-final, which saw Hernandez and American pair Nick Baumgartner and Mick Dierdorff advance, the stage was set for a mouth-watering finale.
Baumgartner and Dierdorff were then involved in another collision, this time with Pullin, leaving the path free for Vaultier, who crossed the line ahead of Hughes and Hernandez to retain his title.
Speaking to Reuters after the final, Vaultier said it felt different crossing the line compared to how it had at Sochi four years ago.
"It is not the same flavour," Vaultier said. "I came into Sochi with outsider status and today I was the leader. It is really great to defend my title but it was way harder.
"I didn't have anything to lose in Sochi, today I had everything to lose and I won it."
Vaultier also became emotional speaking about the fall in the semi-final that almost cost him a place in the final.
"That was terrible, it was really insane. I thought now everything is finished," he admitted. "It was a stroke of luck I could continue and qualify in third place."
The 30-year-old added that he was unlikely to come back in four years to defend his title in Beijing.
"I just don't know if I can put my body through it," he said. "It is hard to commit for another four years as I have family back home. It takes huge energy to work away from my family. I am happy if it all ends up like this."
(Reporting by Jack Tarrant)
