The two chiefs of staff, Major General Mohammad Bagheri and General Valery Gerasimov, "condemned the American operation against a Syrian air base which is an aggression against an independent country", state news agency IRNA said.
The American strikes "aim at slowing the victories of the Syrian army and its allies, and reinforcing terrorist groups", they said in a statement.
Trump orders strikes on Assad airbase
The two army leaders vowed to continue their military cooperation in support of Syrian President Bashar al-Assad "until the total defeat of the terrorists and those that support them", according to the Mehr news agency.
Iran and Russia are Assad's closest allies and label all opponents of his regime as "terrorists".
Don't shift blame for Syria gas attack, say senators to Trump
Both governments have defended Assad against Western allegations that his regime carried out a suspected chemical weapons attack on the rebel-held town of Khan Sheikhun on Tuesday, killing dozens of civilians.
President Hassan Rouhani earlier criticised his US counterpart Donald Trump for the missiles fired early on Friday in response to the suspected chemical attack.
"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.
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