Vladimir Putin, Russia's president, and Mikhail Saakashvili, Georgia's leader, agreed to resume flights when they met last month.
However, many other tensions remain in the relationship, principally Georgia's drive to become a member of the Nato military alliance.
There was little sign of a quick warming in relations when Sergey Ivanov, Russian first deputy prime minister, said on Tuesday that Georgia would have to repay $3m in air control fees.
Zoia Morchiashvili, a passenger on the Airzena-Georgian airways flight to the Russian capital, said: "It's very important that flights have been resumed... My family and relatives live here. Communication is very important."
Moscow cut air, sea and postal links with Georgia in October 2006 after a spying row triggered a sharp deterioration in relations between the countries.
Russia also halted Georgian wine and mineral water sales, which were crucial exports for the Caucasian country.
In a further move in 2007, Moscow doubled Tbilisi's gas bill to $235 for 1,000 cubic metres.
Apart from two charter flights linked to religious holidays, the only other flights between the two countries since the ban have been aircraft deporting Georgians deemed by Russia to be illegal immigrants.
Travellers flying between Moscow and Tbilisi have had to take alternative routes through other cities such as Kiev, Baku or Istanbul.
Russia says Georgia's policies in the region are aggressive and it is failing to be a good neighbour to Russia.
Georgia said the Kremlin was punishing it for its push to join Nato and the European Union.
It also says Moscow is propping up its breakaway regions of South Ossetia and Abkhazia, and using them to try to stymie its Nato bid.
Following his disputed re-election in January, Saakashvili said he would work to improve ties with Moscow and Sergey Lavrov, Russia's foreign minister, subsequently attended his inauguration ceremony.