Gazprom Neft did not disclose the value of the deal.
Gazprom Neft now holds 51.69% of Sibir Energy, the company said.
In July, Gazprom Neft sold a 3.02 percent stake in Sibir Energy to the Moscow government.
Sibir Energy's core assets are the Salym oil fields in the Siberian Nefteyugansk area, operated together with Dutch Shell via a joint venture. The company also holds slightly less than 50% of shares in the Moscow Oil Refinery and 138 filling stations in the city of Moscow.