It does not specify that the safe zones take effect immediately, but gives the three guarantor countries two weeks to form working groups to delineate them and then until June 4 to come up with their definitive boundaries.
Russian Foreign Minister Sergey Lavrov and US Secretary of State Rex Tillerson shared a phone call Friday discussing the zones, the Russian foreign ministry said, according to Russian state media news outlet TASS. But the full details of the proposal were not made available and prospects for its success appeared bleak.
Iran says it is a massive step toward the de-escalation of the long-standing conflict and bloodshed in Syria.
The walkout and the comments underline the huge difficulties of implementing such a deal.
A previous cease-fire agreement that went into effect on December 30 helped reduce overall violence in Syria for several weeks but eventually collapsed. Other attempts at a cease-fire in Syria have all ended in failure.
The deal excludes the terror-designated groups such as the Islamic State (IS) group and the al-Qaida-linked Nusra Front, as the battles against those groups will continue. Rebels fighting to topple Assad are enraged by Iran's role in the deal and blame the Shiite power for fueling the sectarian nature of Syria's conflict, now in its seventh year.
The agreement would create four cease-fire zones in northern Syria where fighting would stop by Saturday to provide civilians a place to gather to escape the violence and receive food and medical attention.
The U.S. military has conducted air strikes in the past in one of the proposed "de-escalation" zones in Idlib, home to a group affiliated with the al-Qaeda terror group.
There were reports that the safe zones would be no-fly areas for warplanes from the US-led coalition.
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The US State Department said that it supports "any effort" that can genuinely move toward peace but voiced scepticism about the new agreement's ability to create safe zones. That arrangement was suspended last month after the U.S. Tomahawk missile barrage on a Syrian air base, fired in response to a deadly chemical gas attack in Syria that was blamed on Assad's government.
The ministry said the Syrian government's approval comes out of its concern for the lives of the Syrians. But some delegates from the rebel forces angrily rejected the plan.
The second is in the north of central Homs province, where rebels hold a stretch of territory, with the third covering the eastern Ghouta area, a rebel stronghold outside the capital Damascus.
The deal - which was agreed on Thursday and published today - will see four "de-escalation zones" established for a period of six months.
A war monitoring group said there were no initial reports of casualties. "All Syrian flights over these areas will cease".
Ahmad al-Masalmeh, who is based in the southern province of Daraa that borders Jordan, said there were six breaches in the province when government forces shelled opposition-held areas. He spoke at a press conference shortly after delegations of the three sponsor nations signed the agreement in the presence of de Mistura. Both countries support Syrian president Bashar al-Assad.
"If this (negotiating) table does not lead to solutions, we will return to the gun", he said.
Fighting has continued in parts of Syria covered by a controversial Russian-sponsored ceasefire plan, which came into effect at midnight on Friday.
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