Few expected a breakthrough, but Moscow said talks were needed as tensions in Europe are “off the scale”.
Russia has moved thousands of troops to the border, but insists it has no intention of attacking Ukraine.
It wants guarantees Ukraine will not join Nato, but Western powers say Kyiv’s sovereignty should be respected.
The talks began at 10:07 US Eastern time (15:07 GMT; 18:07 Moscow time), the White House said.
They were held on a secure video link set up under previous administrations but never used before, Russian news agency Tass said.
Mr Putin held the talks from his residence in the southern resort of Sochi, according to Tass.
Mr Biden and Mr Putin last met in person in Switzerland in June, but made little progress other than to agree to send their ambassadors back and begin a dialogue on nuclear arms control.
In a conference call on Monday night, the White House said the leaders of the US, UK, France, Germany and Italy had formed a joint strategy “to impose significant and severe harm on the Russian economy” should Russia launch an invasion.
Mr Biden is expected to speak to the four European leaders again after his talks with Mr Putin.
Possible measures include restrictions on Russia’s banks converting roubles into foreign currencies, or even disconnecting Russia from the Swift global financial payment system, reports say.
Russia wants guarantees that Ukraine will not try to seize areas captured by Russian-backed separatists in 2014 and has warned the West not to cross “red lines” by adding Ukraine to Nato’s military alliance.
More than 90,000 Russian troops are believed to be massed near Ukraine’s borders.
A large part of the recent Russian military build-up is in Crimea, which Russia seized from Ukraine and then annexed in 2014.
Troops are also gathering near Ukraine’s eastern Donbas region, the name for parts of Luhansk and Donetsk regions which are under the control of Russian-backed separatists.
Ukrainian officials have said Moscow could be planning a military offensive at the end of January.