Michael Messerly, a fan who witnessed the crash, said it appeared Stewart hit the driver as he was walking on the dimly lit track after they had collided on the previous lap.
He said the driver was wearing a dark racing suit as Stewart's car passed him.
"I didn't see (the other driver) anymore," he said. "It just seemed like he was suddenly gone."
Messerly said the crash appeared to be the result of "a number of bad decisions" and not "any intent on Tony Stewart's part."
"Auto racing is a dangerous sport," he said. "I think it was just an unfortunate set of circumstances that created a tragic situation."
The track, about 30 miles southeast of Rochester, canceled the remainder of the race within five minutes and later posted a message on its Facebook page encouraging fans to "pray for the entire racing community of fans, drivers, and families."