The men's bodies were found south of the Mangatawai Stream between 1pm and 2.30pm, a police spokesperson said.
Three teams consisting of a dozen people were searching the area.
"Police were committed to finding the men," the spokesperson said.
Police thanked everyone who assisted with the search.
"It is important that we have been able to bring the men back to their whanau to provide them with a sense of closure at this difficult time," Senior Constable Barry Shepherd said.
The men's deaths will be referred to the Coroner.
Vincent Taurima and Hakopa Ngaronoa disappeared in the park on August 12.
They were allegedly driving a stolen vehicle, prompting the police chase, before disappearing into the bush off Tree Trunk Gorge Rd, near the Desert Rd.
The following day they made contact with police, saying they were lost and cold and needed help.
Previous searches uncovered a campfire, a pair of shoes, two piles of clothing and a beanie.
Police have previously voiced serious concerns for the men's welfare considering their lack of experience in the bush and the inappropriate clothing they were wearing.
Searches had concentrated on the far eastern edge of the Tongariro National Park.
The police spokesperson said the search for the pair had never been called off.
Taupo police senior sergeant Tony Jeurrison said police were grateful to have been able to bring the men home to their whanau.
He described the search as "extraordinary" due to the length of time and number of groups involved.
"Police are obligated to exhaust all avenues when they are searching for missing people. That's the mandate that we have to operate by.
"We told the whanau from the very first day, the whole purpose of the search was to find these two men and bring them home, and we're very grateful to have been able to do that."
The full circumstances of how the men came to be lost would be canvassed in front of a coroner, and he was unable to comment further, he said.
He added that the search had been difficult because of the vegetation, and the weather conditions, which had been wet and cold.
He praised the various search teams for their planning and execution of the search.
"They've been alongside us from day one."
