The talks come as Damascus steps up its military campaign against both the Islamic State group and rebels in second city Aleppo whom it accuses of colluding with Al-Qaeda's Syria affiliate Al-Nusra Front.
Iranian Defence Minister General Hossein Dehghan said he and his counterparts from Russia and Syria were determined to deliver a "decisive" battle against "all terrorist groups".
Dehghan said the goal could be achieved by "blocking or preventing" these groups from receiving political support or weapons that could enable them "to conduct wider operations".
The fight against "terrorism" must be done based on "a mutual programme and specified priorities," he said after the talks, the results of which should be seen "in the coming days".
"We made decisions for what must be done on the regional and operational levels in an agreed upon and coordinated manner," state television website quoted Dehghan as saying.
"The terrorists and their supporters must know that the group fighting against them is determined to support this route until the end and will do so.
"The first step toward restoring security to the region is comprehensive ceasefire" and humanitarian aids, said Dehghan.
"We agree to a guaranteed ceasefire that doesn't lead to the strengthening of terrorists in this country," he said, adding that "supporting the Syrian army forces" was another major topic.
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A Russian defence ministry statement before the meeting said talking points were "priority measures in reinforcing the cooperation between the defence ministries of the three countries in the fight with Islamic State and Al-Nusra terrorist groups."
Iran and Russia are Syria's main allies against the various armed groups fighting Assad, including IS jihadists.
Moscow has sent warplanes and special forces in support of his regime, while Tehran has deployed military advisers and trained and equipped pro-government militias.
The visit of Russia's Defence Minister Sergei Shoigu comes after Moscow's pledge to step up its air strikes against rebel forces in and around Aleppo.
Tehran has provided Damascus with military and financial support ever since the uprising against the Assad regime erupted more than five years ago.
Assad's position in the battle field received a major boost after Moscow intervened to help last September.
Russian forces helped government troops recapture the famed ancient city of Palmyra in March and are now backing a push towards Syria's largest dam at Tabqa in the Euphrates Valley.
Shoigu was also expected to hold separate bilateral meetings with Syrian General Fahd Jassem al-Freij and General Dehghan.
In a meeting with Shoigu, Iran's secretary of Supreme National Security Council Ali Shamkhani thanked "the courageous actions and policies of Russian President (President Vladimir Putin) and his effective support in the comprehensive fight against terrorism in Syria".