"Greetings, Mr. President," Putin said in a brief video clip released by the Kremlin. Biden said it was "good to see" his Russian counterpart, adding that he hoped their next session would be in person.
Despite the friendly opening scene, the summit, lasting just over two hours, was steeped in tension.
Russia denies planning to invade Ukraine, but with satellite pictures showing massive troop concentrations on the border, fears are growing of war in Europe.
Reflecting the brittle atmosphere, Biden sat behind closed doors in the White House's high security Situation Room. By contrast, Biden held a similar video summit with Chinese President Xi Jinping three weeks ago in the more decorative Roosevelt Room, with journalists invited to witness the opening minutes.
The United States says it doesn't know for sure what Russia intends to do in Ukraine, but is alarmed at the deployment of some 100,000 battle-ready Russian troops to the border. Russia already supports a powerful separatist rebellion across swaths of eastern Ukraine and annexed the Crimean peninsula from Kiev in 2014.
Moscow calls invasion talk "hysteria." Instead, Putin intends to tell Biden he sees Ukraine's growing alliance with Western nations as a threat to Russian security -- and that any move by Ukraine to join NATO or to host NATO missiles would be unacceptable.
Even though Ukraine is nowhere near being able to join the US-led military alliance, Putin wants a "legal" guarantee this will never happen.
"Russia has never planned to attack anyone," Kremlin spokesman Dmitry Peskov said Tuesday. "But we have our own red lines."
The United States and NATO say Russia cannot be given a veto over Ukraine's ambitions.
The White House said Biden and Putin, who last met in Geneva in June, began their video summit at 1507 GMT -- 10:07 am in Washington and 6:07 pm in the Black Sea resort of Sochi, where Putin has a residence. The Kremlin announced it had ended at about 1715 GMT.