The man's body was discovered at a depth of 95 metres by a robot operated by members of the Geneva cantonal police force, according to a news release from the Vaud cantonal police.
The victim's wife had contacted police on Saturday at around 9pm saying that she had not heard from her husband since he told her earlier in the day that he intended to dive in the lake in an area near the Chateau of Chillon.
The resident of the Morges area, west of Lausanne, had planned to dive with a friend but the friend decided not to go, police said.
Riviera region officers on Saturday discovered the diver's car in the lakeside municipality of Tour-de-Peilz, near Montreux.
The vehicle was found near an area known as an access point for divers seeking the wreck of the Hirondelle, a passenger steamboat which sank in 1862.
The boat, which at the time was the biggest boat on Lake Geneva completely built in Switzerland, capable of carrying 800 passengers, lies at a depth of up to 60 metres below the surface.
A search was launched involving a Rega emergency helicopter and a lifeboat crew from Terriet on Saturday night, police said.
Weather conditions did not initially allow for a submarine search.
But early Sunday morning, a border patrol boat, a Vaud cantonal police boat and six divers from the Vaud gendarmerie resumed the search, along with officers from Geneva's electronic search unit, using a robot, police said.
The robot ultimately found the man's body.
A website dedicated to divers seeking to visit the Hirondelle shipwreck warns that access is difficult and dangerous for divers who are not very experienced.
It notes that the shipwreck is tilted on a steep slope and that visibility is often poor, while advising anyone diving there for the first time to go with someone who knows it well.
The vessel sank without loss of life after striking a rock close to shore.
The shipwreck was discovered by divers in 1966 and subsequently became a popular attraction for experienced divers.