"This is a large-scale project for Russia," Putin said at the official ceremony in the port of Sabetta on the Yamal peninsula beyond the Arctic Circle.
The centrepiece of the event was the loading of the first gas shipment onto an icebreaking tanker from the Yamal LNG plant, with temperatures of minus 28 degrees Celsius (minus 18 degrees Fahrenheit) outside.
For the project, Russia's privately owned gas producer Novatek partnered with France's Total and China's CNPC.
White whiskers have been painted on it in honour of the late CEO, who was known for his white bushy moustache.
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"I congratulate you all on the first loading of the cargo tanker which is named after our friend Christophe de Margerie," Putin said, praising him as "one of the trailblazers for this project".
"At the start of the project, people told me not to pursue this. Those who started this project took a risk but achieved a result," Putin added, thanking the project's international participants.
The USD 27 billion (23 billion euro) project is set to start with a production capacity of 5.5 million tonnes per year and increase this to 16.5 million tonnes by the start of 2019.