General Valery Gerasimov and Major General Mohammad Bagheri spoke by phone and "condemned the American operation against a Syrian airbase which is an aggression against an independent country", Iran's state news agency IRNA said.
Russia and Iran are Syrian President Bashar al-Assad's closest allies, and label all opponents of his regime as "terrorists".
US warships in the Mediterranean launched a barrage of 59 cruise missiles at Shayrat airbase in Syria early on Friday, after 87 people including 31 children were killed in a suspected aerial chemical attack on rebel-held Khan Sheikhun.
It was Washington's first direct military action against Assad's government.
Another air strike on Saturday on the same town in the northwestern province of Idlib killed a woman, the Britain-based Syrian Observatory for Human Rights reported.
It said it was unclear if the latest strike was by Syrian or Russian warplanes.
The monitor also reported an air strike on Urum al-Joz, another Idlib town, on Saturday that killed 18 civilians including five children, which it said was believed to have been carried out by Russian aircraft.
Idlib province is controlled by a rebel alliance that includes a former Al-Qaeda affiliate, and is regularly targeted by both the Syrian government and its Russian ally.
Russian Foreign Minister Sergei Lavrov accused Washington of "playing the terrorism game", during his first phone talks with his US counterpart Rex Tillerson since the US air strikes on Syria.
- 'Intolerable aggression' -
Speaking on a US talkshow to be aired Sunday, Tillerson insisted he had no concerns about possible retaliation by Moscow as "Russians were never targeted" in the strike and said defeating the Islamic State group was the top priority for the US in Syria.
"Once the ISIS threat has been reduced or eliminated, I think we can turn our attention directly to stabilising the situation in Syria," he told CBS television's "Face the Nation" in a clip released ahead of its air time.
"We're hopeful that we can prevent a continuation of the civil war and that we can bring the parties to the table to begin the process of political discussions," he said, noting that would require the participation of Assad's regime and its allies.
Much of the international community accused Assad's government of carrying out Tuesday's suspected chemical attack on Khan Sheikhun, but Damascus denied responsibility.
North Korea denounced the US attack, calling it an "intolerable act of aggression" that "proves a million times over" that Pyongyang was right to strengthen its nuclear programme.
The statement by the Iranian and Russian military chiefs said they would continue their military cooperation in support of Assad "until the total defeat of the terrorists and those that support them", according to Iran's Mehr news agency.
The US strikes "aim at slowing the victories of the Syrian army and its allies, and reinforcing terrorist groups", they said in a statement.
Both Tehran and Moscow have defended Assad against Western allegations that his regime carried out the attack on Khan Sheikhun.
- 'Terrorists celebrating' -
Iran's President Hassan Rouhani Saturday criticised his US counterpart Donald Trump for the missile attack on the Syrian airbase.
"This man who is now in office in America claimed that he wanted to fight terrorism but today all terrorists in Syria are celebrating the US attack," he said.
As the Arab League on Saturday warned against a "dangerous escalation" in Syria, influential Iraqi Shiite cleric Moqtada Sadr called on Assad to step down and on Washington and Moscow to stop intervening in the conflict.
"I would consider it fair for President Bashar al-Assad to resign and leave power, allowing the dear people of Syria to avoid the scourge of war and terrorist oppression," he said.
Several Iraqi Shiite militias, some of them directly supported by Iran, are helping Assad's camp by sending fighting units across the border.
More than 320,000 people have been killed in Syria since the conflict erupted in March 2011 with anti-government demonstrations.