Wilson was airlifted out of the track with a severe head injury after he was hit by a large piece of debris that broke off Sage Karam's car when Karam spun into the wall. IndyCar announced Wilson was in a coma and in critical condition.
Karam was taken to a hospital with an injury to his right foot.
IndyCar had a subdued Victory Lane, and Hunter-Reay was not sprayed with the traditional confetti.
The race resumed after the Karam and Wilson accident, and Hunter-Reay picked his way through the field. He passed Juan Pablo Montoya and Takuma Sato, and then used a bold inside pass of leader Gabby Chaves to take the lead with five to go.
Chaves appeared to have an engine failure that brought out the caution with three to go. The race ended under yellow.
Josef Newgarden was second, and IndyCar points leader Montoya finished third.
Vautier was on the low side as he tried to go three-wide and ran out of room, sending both drivers up the track and into the wall.
"There was nowhere to go," Vautier said. "I'm the bad guy when this happens."
Rahal was livid. He hopped out of the No. 15 Honda and walked on the track to confront Vautier. Rahal removed his helmet and pointed and shouted at Vautier before the drivers were separated.
"Unfortunately, I was driving against a guy there who isn't using his head," Rahal said.
IndyCar warned drivers before the race to stay clear of the ones in contention for a better shot of a clean finish with only two races left in the season. Rahal finished 20th.
"We were still in a good spot," Rahal said. "The real shame of it is that it's a Honda that took us out. That's the real shame because he probably just ruined Honda's chances of winning the championship."
Montoya's cushion grew from nine points to 35 with next Sunday's finale in Sonoma set to decide the title.
The finale is worth double points, and six drivers will head to California in contention for the title. Hunter-Reay is mathematically eliminated, but he picked up his second win of the season in what has been a disappointing year for Andretti and Honda.
The Associated Press contributed to this report.