President Vladimir Putin received Lavrov and Tillerson at the Kremlin Palace, spokesman Dmitry Peskov told reporters later.
The polarised positions were evident at the UN Security Council on Wednesday, when Russian Federation vetoed a Western-drafted resolution that would have required Syrian cooperation in an investigation into the suspected chemical attack.
Both disagree on the approach to Syria and traded words over what exactly should be done.
"This is just the latest in a series of the use of chemical weapons by the Assad regime".
He called the USA military action "genius", and stated that Xi, too, "was OK with it".
But Lavrov stood firm, saying that "removing or ousting" anyone from power was not on Russia's agenda.
The United States has said that Syrian President Bashar al-Assad is responsible for a chemical weapons attack on his people that left dozens dead. He says both countries have agreed that their lines of communications must stay open. Tillerson's mission sees the Trump administration taking on the traditional USA role as spokesman for a unified Western position.
"We have seen very alarming actions recently with an unlawful attack against Syria", Lavrov said, referring to the 59 Tomahawk missiles Trump launched at an air base to punish Assad for using chemical weapons.More news: Diego Costa 'happy' at Chelsea but future questions remain amid London hint
The motion was put forth by Western powers who blame Assad for the attack.
In an exclusive video interview with the Agence France-Presse (AFP) news agancy, Mr Assad said "there was no order to make any attack".
But Mr Lavrov argued that this would only help Islamic militants.
Russian Federation did not pull any punches with the U.S. during this crucial visit. However, while Lavrov said that he didn't want to "shield anyone", he asserted once again that Russian Federation didn't believe the Syrian government was behind the chemical attack in the town of Khan Sheikhoun in Idlib, Syria.
"We believe it is fundamentally important not to let these actions happen again".
Any hope in Russian Federation that the Trump administration would herald less confrontational relations has been dashed in the past week after the new USA leader fired missiles at Syria to punish Moscow's ally for its suspected use of poison gas. The Syrian people "have suffered six years of ever-escalating barbarity, over six years of failed ceasefires, and over the years, Russian Federation has held us ransom for the Assad regime". The Kremlin had previously declined to confirm Putin would meet Tillerson, reflecting tensions over the USA strike on Syria.
"Despite the quantity of existing problems. there are considerable prospects for joint work", Lavrov said, after he took Tillerson for private talks with Putin.
WASHINGTON, D.C. - With tensions rising over Syria and other issues, President Donald Trump said Wednesday that US relations with Russian Federation "may be at an all-time low" as he moved ever further away from his campaign promises to establish better ties with Moscow.