The Otago Daily Times reported the car crashed through a fence and came to rest in a field.
The newspaper said the second suspect was found by a police dog unit hiding in reeds, after a search using a helicopter and a thermal imaging camera and police today said thank you to locals who gave information.
Max Gooch, of Sydney, was a customer in the store during the robbery and told the Otago Daily Times he saw a man with blood on his face.
The bloodied man "didn't say a word" during the robbery, Mr Gooch said.
"I went to the counter to pay, and the guy behind the counter gave me a really weird look."
Mr Gooch "grabbed" his girlfriend and the couple left the store.
"The guy walked off really calmly."
Two men, aged 17 and 24, will appear in the Queenstown District Court this morning.