The launch is a major milestone for Russia's beleaguered space sector, with the new spaceport in the country's far east touted to mark a rebirth of an industry plagued by a string of embarrassments in recent years.
Carrying three satellites, the Soyuz 2.1a rocket took off at 11:01 am, the Roscosmos national space agency said in a statement, after the countdown was automatically halted for technical reasons 24 hours previously.
Putin was present for the take-off.
"You know they say that the proof of the pudding is in the eating. You have to make the first launch to confirm the cosmodrome is ready for work. And you did it!" Putin told industry officials.
"I want to congratulate you. We can be proud. It's a serious and important contribution to the development of the Russian space industry," he added.
"Yesterday the technical side was put to the test and the launch had to be stopped, but it happens. It's a normal thing."
A European launch from French Guiana had to be put off three times last week before finally taking place on Monday.
The Russian delay was due to a malfunction of a cable, space agency spokesman Mikhail Fadeyev, told AFP.
Putin officially reprimanded Dmitry Rogozin, the Deputy Prime Minister in charge of the space and defence industries, and Roscosmos head Igor Komarov over the delay, his spokesman told reporters.
Construction on the new spaceport began in 2012 but has been marred by labour disputes, corruption scandals and delays.
"Despite all its failings, Russia remains the world leader in the number of space launches," Putin told a meeting of space officials yesterday.
"But the fact that we're encountering a large number of failures is bad. There must be a timely and professional reaction.
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