The Russian strongman, who enjoys venturing into the wilderness and has accompanied an expedition to track polar bears in the Arctic, was the first recipient of a symbolic water sample.
"The head of the natural resources ministry has given Vladimir Putin the first sample of prehistoric water the Russian polar expedition extracted from the subglacial lake in Antarctica," the Russian government said.
"The age of the water could be over 1 million years," it said.
Natural Resources and Ecology Minister Yury Trutnev handed Putin a small glass container containing a yellowish liquid with the inscription "Lake Vostok, aged more than 1 million years," the state RIA Novosti news agency reported.
With characteristic dry humour, Putin asked Trutnev whether he had tried drinking the water.
"No," Trutnev answered.
"That would have been curious. Dinosaurs drank it and Trutnev," Putin said in comments released by the government.
A Russian expedition on Sunday sunk a borehole down to the surface of the pristine subglacial fresh water lake, hidden under almost 4 kilometres (2.3 miles) of ice and raised a column of water for scientists to study.
Putin, who is planning to reclaim his old Kremlin job in March elections, called for the scientists behind the discovery to be decorated.
"This is a major event. We need to think how to honour these people," he said.
The water given to Putin probably did not come from the main body of the lake, but was frozen lake ice raised from the borehole just before it reached the lake's surface, an expert behind the project told RIA Novosti.
"This water was apparently received when they lifted the ice core from the last section of the borehole. And that really is water from Lake Vostok," said Valery Martyshchenko of the hydrometeorology and environmental monitoring agency.
The costly project is a rare triumph for national science and has excited scientists around the world with its potential for discoveries of new forms of life and revelations about millions of years of the Earth's history.