The remains, a backpack and notebook believed to belong to Laundrie were discovered on Wednesday in a Florida wilderness park, according to the FBI.
The area where they were found had been under water during earlier searches.
The FBI's Denver office said in a news release on Thursday that a comparison of dental records confirmed that the remains were Laundrie.
The discovery of the remains concluded a massive search involving federal, state and local law enforcement that began shortly after Laundrie disappeared on September 14, two weeks after the 23-year-old returned alone to his parents' home in North Port, Florida.
Petito's family reported her missing September 11, launching a search that garnered worldwide media attention and focused largely on the Carlton Reserve wilderness park near the Laundrie home.
It is a densely wooded, swampy area that is home to alligators, coyotes, bobcats, snakes and numerous other creatures.
The intense focus on Petito's case has led to renewed calls for people to pay greater attention to cases involving missing Indigenous women and other people of colour.
The body of Petitio, 22, was found September 19 on the edge of Wyoming's Grand Teton National Park, which the couple had visited.
The coroner there concluded she died of strangulation and her body had been where it was found for three or four weeks.