According to the Minneapolis Star Tribune, Isaiah was last seen playing with his 7-year-old brother at his home. He was missing for more than 24 hours until the car's owner came to pick it up from the shop.
Police officers had searched inside and under the car, but had not looked in the trunk.
"Obviously, this is pretty much the worst ending we could have come to," Sheriff Peter Johnson told reporters Friday. "The only thing worse would have been if we had never found him."
Johnson also called his conversation with Theis' parents "one of the worst things" he had ever had to do.
KARE TV said Friday that authorities are still investigating how Isaiah got into the trunk, though the autopsy showed no signs of traumatic injury or disease.