The discovery of the bodies brings to five the number of known dead after the luxury ship ran aground with some 4,200 people aboard on Friday night.
The Coast Guard said Sunday the bodies of the two elderly people were found in the submerged restaurant.
Earlier Sunday a helicopter airlifted a third survivor from the capsized hulk of the ship.
As divers searched the waters surrounding the Costa Concordia, crews in dinghies were touching the hull with their hands near the site of the 160-foot-long gash in its side, the Associated Press reported.
Three people — two French tourists and a Peruvian crew member — were confirmed dead after the massive cruise ship ran aground on Friday night with some 4,000 passengers on board, according to the AP.
Around 40 more remain unaccounted for, however CNN quoted Giuseppe Orsina of the local civil protection agency as saying: "These people could be still on the island of Giglio, in private houses or in hospitals.
Firefighters reportedly earlier rescued a South Korean couple on their honeymoon after hearing their screams coming from a section of the ship still above water.
Meanwhile, the cruise ship's captain, Francesco Schettino — who has 11 years of experience with the company — was being investigated on allegations of manslaughter and abandoning ship, CNN cited chief prosecutor Francesco Verusio as telling Italy's ANSA news agency.
First officer Ciro Ambrosio had also been detained and might face similar charges.
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At issue was how the Costa Concordia could stray so close to the island of Giglio, given how well mapped Italy's sea lanes are.
CNN cites Italian Coast Guard Capt. Cosimo Nicastro as saying the cruise ship was 2.5 miles off-route when it struck the rocky sandbar.
The impact ripped a hole in the cruise ship's hull, forcing passengers and crew to escape in what the AP described as "a chaotic, terrifying evacuation."
"There are rocks, they are on the maps," Nicastro said, according to CNN. "What we know is the ship went really close to these rocks. ... We don't yet know why."
The ship began taking on water Friday night, and the crew kept going because they believed the vessel could continue sailing normally, Nicastro said.
Authorities are also investigating why the ship didn't issue a mayday call.
ANSA reportedly quoted Francesco Schettino's sister, Giulia, as saying her brother called their mother, 80-year-old Rosa, at 5 a.m. and said, "Mamma, there has been a tragedy. But stay calm. I tried to save the passengers. But for a while, I won't be able to phone you."