The conversation was initiated by the American side, the statement said.
"Lavrov stressed that an attack on a country whose government is fighting terrorism only plays into the hands of extremists [and] creates additional threats to regional and global security," it said.
President Donald Trump ordered a missile strike against the air base earlier this week, targeting it because the Syrian jets that carried out the bombing of a rebel stronghold with chemical weapons Tuesday originated there, US officials said. The attack injured hundreds, killing nearly 90 people, including almost 20 women and more than 30 children, according to Syrian health officials and Syrian Civil Defense volunteers.
Russia's Ministry of Foreign Affairs added that Lavrov emphasized on the call that the allegations of chemical weapons use by the Syrian military "do not correspond to reality" and called for a "thorough and impartial" investigation into the incident.
In an earlier statement
, the Kremlin said Syria "has no chemical weapons," pointing to reports by UN inspectors.
"(Russian President) Vladimir Putin believes that complete disregard for factual information about the use by terrorists of chemical weapons drastically aggravates the situation," the statement said. "This move by Washington has dealt a serious blow to Russian-US relations, which are already in a poor state."
Tillerson and Lavrov agreed to continue the discussion about Syria in person, the ministry's Facebook post Saturday said. Tillerson is due to meet Lavrov in Moscow next week.
A State Department official confirmed to CNN that Tillerson called Lavrov on Saturday to discuss his upcoming visit to Moscow but would not provide further details about the conversation.
Putin denounced the US strike against the air base as "aggression against a sovereign state in violation of the norms of international law."
The Russian Defense Ministry said Friday that it plans to bolster and increase the effectiveness of the air defense system in Syria following the attack.
"In order to protect the most sensitive objects of the Syrian infrastructure, a system of measures to bolster and increase the effectiveness of the Syrian armed forces' air defense systems will be implemented," ministry spokesman Igor Konashenkov said in a statement carried on state media.
Iranian President Hassan Rouhani also spoke out about the US strike on Saturday and similarly called for "impartial countries" to form a "fact-finding commission to find out about how and through which border chemical weapons entered Syria."
Rouhani made the comments while speaking at an economic and agricultural conference in Tehran.
"Those who have taken over US affairs once claimed they wanted to combat terrorism; however, today Syria's terrorists are happy about [the] US invasion in Syria and are celebrating it," he said.
"These people did not ask for permission even from the UN and their own Congress, which we believe are flawed, and ignored all international principles and laws, attacking Syria with aggression, blatantly and outrageously," Rouhani added.
North Korea's Ministry of Foreign Affairs, meanwhile, said the US strikes on the air base "can never be tolerated" and were a "clear act of invasion against a sovereign country," the communist government's news arm reported.
"The world is clearly witnessing who is the peace-breaker and destroyer through this military attack of US to Syria," the statement said, according to the Korean Central News Agency.
Pyongyang also said the US strike justified the development of North Korea's nuclear weapons program, the state-run news agency said, similarly calling the missile strike an "invasion" effort.
"Our great military power with nuclear at its core is being the sword of justice that destroys US's shameless abuse of power and invasion maneuver, safeguarding the country's sovereignty and the people's right to live. Today's reality proves that our choice to strengthen our nuclear power and to stand against force with force was right a million times over," the report said.