The 285km (178-mile) pipeline will go overland from Bulgaria’s Black Sea port of Burgas to the northern Greek town of Alexandroupolis on the Aegean Sea.
The deal caps negotiations that have lasted 13 years.
A Russian consortium will hold a 51% stake in the pipeline. It is expected to be ready in three years’ time.
The consortium brings together state oil firm Rosneft, pipeline monopoly Transneft and a subsidiary of gas giant Gazprom. Bulgaria and Greece will each have 24.5% stakes.
Prime Ministers Costas Karamanlis of Greece and Sergei Stanishev of Bulgaria joined Mr Putin at the signing ceremony in the Greek capital.
The pipeline project’s estimated cost is 900m euros (&pouns;616m; $1.2bn).
Russian tankers are frequently held up for 10 days at a time as they wait to navigate Turkey’s narrow, congested Bosphorus and Dardenelles Straits.
The removal of these delays should help to bring oil costs down, the BBC’s Malcolm Brabant reports from Athens.
Pipeline diplomacy is helping to reassert Russian influence in the region, he says.
Earlier this month a senior US State Department official, Matthew Bryza, was in Athens and congratulated the three signatories to the pipeline accord.
He said the more oil that reached global markets the better. But Mr Bryza added that the United States was concerned that Europe could become too reliant on the Russian energy giant Gazprom as a source of natural gas.
At least one third of Russian oil exports currently leave by tanker via the Black Sea and Bosphorus Strait.
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