He auctioned off the precious prize in 2014 to raise money for his universities. The medal was purchased in December by Russian billionaire philanthropist Alisher Usmanov.
On Wednesday, head of the Russian Academy of Sciences Vladimir Fortov returned it to the winner as a token of respect.
"The Russian nation through Alisher Usmanov has sort of said thank you for your scientific research, writing books, and promoting science all over the world. So it is nice to feel well liked and respected," Watson said as he reunited with the prize in Moscow.
"I’ve always liked the Russian people and the Russian culture, it is wonderful to be back in Moscow," the scientist said. "I sold the medal because I wanted to say thank you to the institutions which gave me scholarships and let me have a very productive life, so I gave money to my universities."
The 87-year-old underlined that he sold the medal to "do something while I was alive rather than dead."
The medal fetched $4.1 million at a Christie's auction on December 4. It was in a bank for over 50 years.