"There are 12 passengers on board the Mikhail Svetlov," said the port's deputy director, Simon Mamaladze.
The ship has passenger capacity of 112 people. A one-way ticket from Sochi to Batumi costs about $100.
Moscow imposed a transportation and postal blockade on the South Caucasus state in October 2006 in an apparent retaliation for the detention on espionage charges of four Russian army officers. Russian officials cited commercial reasons, but Tbilisi called the move politically motivated.
On Tuesday the countries resumed flights between Tbilisi and Moscow, and an Airzena flight landed at Moscow's Domodedovo airport in the evening.
Despite the restoration of sea and air links, tensions remain high between Moscow and Tbilisi. The Georgian Foreign Ministry said on Monday that Russian lawmakers' recent statement on the recognition of Georgia's breakaway republics was direct interference in the country's internal affairs.
Last Friday, the State Duma, Russia's lower house of parliament, proposed that the president and the government consider the issue of whether to recognize the independence of Georgia's breakaway republics of Abkhazia and South Ossetia.