The bodies were those of Ace Kimberly, 45, and his daughter Becky, 17 -- who went missing last weekend along with sons Roger, 13, and Donny, 15, while sailing off the coast of Florida between Sarasota and Fort Myers.
"The two teenage boys are still missing," Case told reporters.
The five-day rescue operation came to an end Saturday afternoon after more than 100 searches covering nearly 34,000 square miles.
"It is with a heavy heart and sincere condolences to the family and friends that I do this," Case said. "This is probably the most difficult decision I ever have to make in this position."
The cause of the tragedy has yet to be determined.
"We don't have any idea," Case said. "We know there was bad weather... It's just difficult when you don't find everything and you don't have anyone left to tell the story."
About 15 family members and friends were notified Saturday of the search's end.
"They're a strong family," Case said. "They all came together. They took it hard but ... they were strong. A lot of them reacted more strongly than I think I would."
The Florida Fish and Wildlife Conservation Commission is conducting an accident investigation.
Daughter wore life jacket, father did not
A Cape Coral Fire and Rescue team found one body Thursday morning, east of Boca Grande. It was located about 4 miles southeast of the location where crews found a body in a life jacket late Wednesday afternoon, according to the Coast Guard. Becky Kimberly was wearing a life jacket, her father was not.
Shortly after the second body was found, a Customs and Border Protection aircraft spotted a sail mast about 100 miles off of Fort Myers' shore.
The Coast Guard also found a bucket containing personal items -- birth certificates, a GPS, wallet, cigarettes, mobile phone, pool noodle and toolbox -- about 5 miles from the location where rescuers discovered the first body.
Missing since Sunday
The family had been living on the 29-foot sailboat in Sarasota for about a year. They were sailing to Fort Myers on Sunday afternoon when they encountered a thunderstorm and rough seas.
The boat, which was equipped with an outboard motor, was "not in the best of shape," and the family was sailing to Fort Myers to work on the sailboat, Case said.
When the storm hit, Ace Kimberly called his brother and asked him to send some weather reports. Kimberly reported 6-foot seas off the coastline of Englewood, about 30 miles south of Sarasota, according to a Coast Guard statement. He was not heard from again.
"He did the best he could," Case said of the brother."He didn't have their exact travel plans... He did a good job in helping us."
The Coast Guard received no distress call from the vessel.
The brother reported Kimberly and his children missing Tuesday. The Coast Guard tracked the voyage, which is about 75 miles via land, and by midmorning Wednesday, an airplane crew discovered a debris field after completing eight search patterns.
A debris field was found 37 miles off Sanibel Island, which sits a few miles off of Fort Myers' coast.
It included water jugs, a tarp, tennis shoes, a basketball and a propane tank, Case said. Rescuers also found life jackets that they believe were among the eight of nine flotation devices the family had on board.
Rescuers also found two kayaks that the family had been towing behind the sailboat.