Racing through heavy rain as well as the fog that had caused the postponement of the event on Monday, the Frenchman edged ahead of his Russian rival over the last two jumps to take the title.
"I took off on the last jump and I don't think I've landed yet," said Vaultier, who was racing with a brace on his right knee after damaging a cruciate ligament two months ago.
"I saw Olyunin on TV and thought, 'this is going to be difficult' ... I was not thinking about becoming Olympic champion, I just wanted to show my full potential."
Olyunin won a popular silver for the host nation and said he was proud to be a pioneer for Russian board cross racers.
"Vaultier is the embodiment of snowboard cross and deserved the gold medal," he added.
Alex Deibold was a wax technician for the United States team in Vancouver four years ago but took a surprise bronze, having edged team mate Trevor Jacob in a photo-finish in the semis.
After being lifted into the air by his better-known American team mates at the finish, Deibold said the miserable weather might have contributed to his third place.
"I've always excelled in adverse conditions, you just have to embrace what mother nature throws at you," the 27-year-old said.
"In U.S. snowboard, we have an A and a B team, and today I've finally made it onto the A team after 10 years."
Stripped of the seeding heats after Monday's postponement, the event still maintained its reputation for unpredictability through four rounds of spills and thrills that saw the early departure of several of the favourites.
Australia's world champion Alex "Chumpy" Pullin crashed out in the quarter-finals and was soon joined at the exit by Austria's former world champion Markus Schairer.
Vaultier knows all about the vicissitudes of his sport after having gone out in the quarter-finals as favourite in Vancouver four years ago and took no chances on Tuesday, winning all three races on his way to the final.
"Being first was the safe way today," said Vaultier. "But being in the fighting group, it was still possible to progress because there were a lot of opportunities."
Olyunin had also won his three races in even more impressive fashion by taking the lead on the early rollers and keeping well clear of the melees in the pack behind him.
Roared on by the locals who had braved the weather, the 22-year-old again sprang out of the gate looking to dominate the final.
Vaultier stuck with him, though, and the pair raced nip-and-tuck over rollers and jumps with first one, then the other, taking the inside track to force themselves ahead on the steeply banked corners.
The Frenchman got the tip of his board in front as the course widened heading into the final jump and, although it was called as a photo-finish, there was no doubt that the 26-year-old from the Hautes-Alpes had crossed first.
There were plenty of falls over the four rounds of racing but only Italian Omar Visintin required serious medical attention after his fall in the second semi-final.
He was taken off the course after clashing with Australian Cameron Bolton, who thought he had broken his wrist, but suffered only the indignity of a badly bruised buttock.