He said the Nord Stream pipeline would reduce Russia's dependence on Ukrainian pipelines, which were shut during gas disputes between Moscow and Kiev.
"Technical gas", needed to build up pressure, was released on Tuesday.
It is expected German consumers will begin receiving Russian gas through the new pipeline in a few weeks.
The official launch of Nord Stream will be marked with a visit by Russian President Dmitry Medvedev to Germany in November.
Nord Stream, a twin pipeline, was built at a cost of $12.5bn (Â£7.7bn; 8.8bn euros) and is 1,224km (761 miles) long, running from Vyborg in north-west Russia to Sassnitz in north-east Germany.
It should be able to move 55bn cu m of gas a year by 2013, after the completion of the second pipeline.
Mr Putin, visiting Vyborg, said Ukraine had been "taking advantage", and that relations between the two countries would now become "more civilised".
At present, 80% of Russia's gas exports to the EU flow through pipelines across Ukrainian soil.
Apart from Nord Stream, Russia has been planning another pipeline, South Stream, which will run from southern Russia to Bulgaria under the Black Sea.
The project is expected to pipe 63bn cu m of gas to central and southern Europe annually.
In another project to pipe ex-Soviet gas westwards, Turkey, Romania, Bulgaria, Hungary and Austria have agreed to construct a 3,900km pipeline called Nabucco.
It is expected to pump up to 31bn cubic metres of gas annually from the Caspian and the Middle East across Turkey and into Europe.
Russian Prime Minister Vladimir Putin has pressed the start button to open a pipeline carrying natural gas directly to Germany under the Baltic Sea.