Speaking at the same news conference, Mr Tillerson admitted the current US-Russia relations were at a "low point" but sounded optimistic about future negotiations on the crisis in Syria.
"It is time to end this brutal civil war, defeat terrorists and allow refugees to return home".
The United States and Russian Federation agreed Wednesday to call for an global investigation of the deadly chemical weapons attack in Syria last week that prompted U.S. President Donald Trump to launch a retaliatory missile strike against the regime of Syrian President Bashar al-Assad.
Tillerson met Putin in the Kremlin after talking to his Russian counterpart, Sergei Lavrov, for about three hours. Though the Kremlin had declined to say whether the leaders would meet, Putin spokesman Dmitry Peskov said Wednesday: "There is a certain likelihood".
Until the chemical attack, the Trump administration had sought to step back from the USA position that Assad should leave power.
Syria's UN Ambassador Bashar Ja'afari said the government is "keen as ever to uncover the real criminal responsible for the use of chemical in Syria", but he told the council the resolution wasn't going to do that because its objective "is to violate Syrian sovereignty". More than 80 people were killed in what the US has described as a nerve gas attack that Assad's forces undoubtedly carried out.
"We discussed our view that Russian Federation, as their closest ally in the conflict, perhaps has the best means of helping Assad recognize this reality", Tillerson said.
Western powers, including the United States, blamed the government of Bashar al-Assad of the attack. Tillerson and Lavrov said in a joint press conference that Syria was a major subject in their discussions.
One of Lavrov's deputies was even more undiplomatic.
After a day of discussions with U.S. Secretary of State Rex Tillerson, Russian Foreign Minister Sergey Lavrov said the former Cold War foes agreed a United Nations probe of events in northern Syria was necessary.
Putin also asserted that Syria has complied with an agreement to dispose of chemical weapons "so far as we know". The two countries remain far apart on a solution for the conflict in Syria.
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Tillerson conceded the two world powers had "sharp differences" that have obstructed cooperation but voiced optimism they could make progress.
In another possible setback to a thaw with Moscow, Trump said on Wednesday that North Atlantic Treaty Organisation is not obsolete, as he had declared during the election campaign past year.
Trump, standing alongside NATO Secretary General Jens Stoltenberg, called on allies to "work together to resolve the disaster" in Syria and thanked them for condemning Assad. "I think it's very bad for mankind", Trump said. Early expectations of an easy rapport between the Trump administration and Russian Federation have crashed into reality as the two countries have traded escalating accusations over what happened last week in a chemical attack in Syria.
"It is perfectly obvious that ... this subject is one we diverge on, inasmuch as Russian Federation is insisting on an objective investigation", Lavrov said. The two diplomats also agreed to appoint special envoys to address some of the "irritants" to relations - which Lavrov pointedly said had developed primarily during President Barack Obama's administration.
"Are we insisting on it? No".
"So I am dismayed that Russian Federation has once again blocked the UN Security Council and in so doing refused to condemn the use of chemical weapons or support a full UN investigation into the attack".
Moscow has stood by Assad, saying the poison gas belonged to rebels, an explanation Washington dismisses as beyond credible.
In the latest veto, Russian Federation blocked a draft resolution backed by the United States, France and Britain to denounce the attack in the town of Khan Sheikhoun and tell Assad's government to provide access for investigators and information such as flight plans.
Such a rider was a nonstarter for all of the resolutions that Russian Federation and China have opposed because it carried the prospect of the forceful removal of Syrian President Bashar Assad.
It was unclear whether Putin, who once gave Tillerson an "Order of Friendship" award, would grant the visiting American an audience in Moscow.
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