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.

Human Rights Watch (HRW) said at least 72 civilians had been killed in the strikes and the bloc needed to bear responsibility where appropriate.
But Nato's spokeswoman said the campaign was conducted "with unprecedented care and precision".
She said Nato "did everything possible to minimise risks to civilians".
"But in a complex military campaign, that risk can never be zero," spokeswoman Oana Lungescu acknowledged.
She added that the alliance "looked into each credible allegation" of harm to civilians and "confirmed that the specific targets struck by Nato were legitimate military targets".
Aircraft from the US, the UK and France conducted most of the 9,658 strike sorties last year, targeting forces loyal to Libyan leader Col Muammar Gaddafi.
The point of the Nato air campaign in Libya last year was to protect civilians, so how many innocent people died is still a sensitive issue, BBC diplomatic correspondent Bridget Kendall reports.
In its report published on Monday
, the US-based HRW said it had examined in detail evidence of claims of civilian deaths from eight separate Nato strikes.
In one instance, it said a first bomb killed 14 people and a second, moments later, killed 18 more who had rushed to help victims.
"We're calling for prompt, credible and thorough investigations," HRW's Fred Abrahams, the main author of the report, told BBC News.
Mr Abrahams says Nato refuses to acknowledge the deaths and has offered no compensation to families.
"Until now, Nato has taken a position of denial," he said.
"I think it will lead to unnecessary civilian deaths in the future if Nato refuses to look at what went wrong and make corrections."
In March, another human rights organisation,  
          Amnesty International, said it had documented 55 cases
 of named civilians, including 16 children and 14 women, killed in air strikes.
It said Nato had failed to investigate these cases thoroughly.
Source: Nato
Adel Ebsat, a relative of three victims who died from an air strike near the eastern town of Zlitan, told the BBC he had repeatedly asked the Libyan government to launch a case against Nato and for an investigation to be carried out.
But there appears to be a reluctance by Libyan officials to hold Nato accountable for any civilian deaths that may have been caused by air strikes, the BBC's Rana Jawad in Tripoli reports.
Most Libyans feel that the alliance helped the country succeed in its uprising against Col Gaddafi, which toppled and killed him last year, our correspondent says.
The overwhelming belief, she adds, is that countless deaths were avoided because of the West's intervention.
Nato has stressed that it is ready to co-operate with the new Libyan authorities in assessing what further action is appropriate.
However, the alliance says it cannot take responsibility because it has had no presence on the ground to confirm the deaths.
Russian Prime Minister Vladimir Putin has pressed the start button to open a pipeline carrying natural gas directly to Germany under the Baltic Sea.
[NEXT_CONCEPT]
Nato has hit back at a report urging the alliance to investigate fully the deaths of civilians in air strikes in Libya last year.