In a statement on its website, the Moscow investigative committee of the general prosecutor's office said that Lebedev "brought bodily harm" to Sergei Polonsky in the incident.
Russian news agencies have said that the charge could result in up to two years in prison.
Lebedev, who owns the UK's Independent and London Evening Standard newspapers, hit property developer Polonsky during a panel discussion in September on Russia's NTV channel about the global financial crisis.
After Polonsky said that he was tired of resisting the urge to give Lebedev "a punch in the chops", the media baron jumped up and threw punches at Polonsky, knocking him off his chair.
Following the attack, Russia's prime minister Vladimir Putin described the incident as "hooliganism", and Polonsky posted photos online purporting to show his injuries from the assault.
However, Lebedev told Russia's Interfax news agency that he only attacked Polonsky out of self defence.
"At one point, expounding on an idea of his and looking straight at me, he said, 'This deserves a punch in the face'," the tycoon claimed.
"I asked 'Do you mean me?', and he shouted 'Yes!' After that, I very neatly neutralised this absolutely unfounded threat."
Polonsky has said that he is considering legal action against Lebedev.
Watch a video of the billionaires fighting below: