Witkoff said in televised remarks at the start of the meeting that he hoped to discuss the resumption of the trilateral talks involving the US, Russia and Ukraine that would allow the technical teams to discuss the next steps towards a peace settlement.
Putin thanked Trump and Witkoff for their efforts to end the war.
The visit on Wednesday came a day after Witkoff met Ukrainian President Volodymyr Zelenskiy and some European leaders in the Norwegian capital, Oslo.
Witkoff's meetings suggested leaders are keen to bring new momentum to US-led peace efforts, more than four-and-a-half years after Russia's army invaded.
The meeting coincided with Russia releasing a retired American teacher who had been jailed on charged of fighting as a mercenary in Ukraine.
The release of Stephen Hubbard had been foreshadowed a day earlier in Washington, when Trump told reporters at the White House that he had talked with Putin "at length" about the issue and had asked him to free the Michigan man.
Efforts by the Trump administration since early 2025 to end the war have made no significant progress, and there was no suggestion of an imminent breakthrough.
Russia and Ukraine are still far apart in their terms for a settlement, as their armies remain locked on the battlefield and they pummel each other with daily long-range strikes.
However, Finnish President Alexander Stubb said late on Tuesday that the Oslo meeting, which he attended, "made genuine progress".
Witkoff and Putin met at St Petersburg's Constantine Palace, and Witkoff said Trump's son-in-law Jared Kushner would join the discussion via a video link.
He said he would inform Putin about Tuesday's talks in Oslo, which he described as "productive", adding that "there is some degree of momentum".
He thanked Putin for lifting Russia's ban on diesel exports, which angered some US lawmakers, adding that it would help reduce prices for US farmers and truckers.
Moscow said the first diesel tanker to the US would be dispatched on Thursday, carrying 40,000 tonnes of fuel, with more to follow.
Putin said he was ready to discuss prospects for the restoration of US-Russian economic ties, adding he was also prepared to discuss the US-led conflict with Iran and using Moscow's relationship with Tehran to bring peace.
Witkoff planned to return to Oslo for more consultations after his trip to Russia, Norwegian Prime Minister Jonas Gahr Store said.
"I think we may have entered a phase now where the Russians are also looking for opportunities for diplomacy," Store told Norwegian broadcaster NRK on Wednesday morning.
Zelenskiy was still in Oslo on Wednesday, where he was visiting the country's parliament and meeting MPs.
Trump said on October 11 that Russia and Ukraine had agreed to a ceasefire in attacks on energy infrastructure but Russia has kept hammering Ukraine's power grid and Kyiv has hit Russian oil refineries.
Russian Foreign Minister Sergey Lavrov said on Tuesday that Moscow was willing to listen to new US proposals about Ukraine but he did not expect any "miracle" from Washington.
At the White House on Tuesday, Trump increased the pressure on Zelenskiy to come to an agreement with Russia as relations between the two men have soured again.
"We want Zelenskiy to make a deal," Trump told reporters in the Oval Office.
"We've given a lot to Ukraine. We've gotten absolutely nothing back except grief, death, tremendous monetary loss."
Amid fears that Washington was turning its back on Ukraine, Zelenskiy said Kyiv was once again receiving early warnings from its partners about incoming Russian missiles, after recent strikes that he said occurred without enough notice from allies.
The change happened after Zelenskiy spoke with his American counterparts, including a phone call with US Secretary of State Marco Rubio.
