Asked on Rossiya-24 television about longstanding rumors that they no longer lived together, the 60-year-old Putin said: "That is true."
Lyudmila Putina, 55, said it had been "our common decision. And our marriage is over due to the fact that we barely see each other."
"It was a joint decision: we hardly see each other, each of us has our own life", Mr Putin said. He said that work of politician requires publicity and someone likes it and others not.
Mrs Putina had rarely been seen in public in recent months, prompting much speculation in Russian media.
She is known to dislike publicity, and told the TV that flying was difficult for her. The divorce was "civilised" and the couple would "always remain close", she added.
Mr Putin confirmed to the TV that the two were no longer living together.
"We have good relations and I am gratitude that he still supports me. Our children have grown up; they have their own lives. Putin always cared about children and they feel his support," Mrs Putina added.
Vladimir Putin and Lyudmila Shkrebneva were married in 1983. They have two daughters, Maria and Yekaterina, both in their 20s.