Authorities in Georgia had been searching for the couple since they went to another part of the state to buy a vintage car off Craigslist.
"It's a sad ending for us here in this community," Telfair County Sheriff Chris Steverson told reporters. "It hurts us to know someone came to our community and met this fate."
Bud Runion, 69, and his wife, June Runion, 66, of Marietta, were last seen on Thursday when they set off for Telfair County in southern Georgia to buy a 1966 Mustang convertible from a purported seller who responded to their ad on Craigslist, Steverson said.
The couple's last telephone call was to a disposable cellphone owned by Ronnie Towns, 28, whom Steverson described as a suspect in the case.
Towns was interviewed by authorities shortly after the couple disappeared and has been charged with criminal intent to commit deception and lying to investigators, Steverson said. Towns turned himself in to authorities on Monday morning, he added.
Towns did not own a 1966 Mustang convertible, the sheriff said.
"I don't think he had a car that was even similar to the one being sought by Mr. Runion," Steverson said.
Before finding the two bodies, search teams combed the rural county about 160 miles south of Atlanta using all-terrain vehicles, aircraft and boats, Steverson said.