The message from Putin was relayed by the head of Russia’s GRU military intelligence agency.
The rebels want all sides in Syria's civil war to allow humanitarian access to those in need and cease attacks on civilians.
The aid said Damascus approved of U.N. resolutions passed last week endorsing an international road map for peace.
Over 100 political and armed opposition factions met to determine Syria’s fate.
An Iranian news agency said yes on Wednesday, but authorities in Tehran and Moscow deny the meeting took place.
As American and French influence declines, the Assad-Iran-Hezbollah-Russia axis rises.
Yet Moscow and Washington's views on the future of Syrian President Bashar-al Assad still diverge.
The military situation on the ground does not indicate that the Assad regime needs to compromise.
His statement appeared to be the first time Moscow said it was aiding Assad's opposition against ISIS.
More than 100 members of Syria's opposition parties and rebel fighting groups are on board.
Islamic State militants have made more than $500 million from black market oil sales.
It is hoped that the factions can form a united opposition ahead of January peace talks with the government.
Syria said four coalition jets killed three of its soldiers and wounded 13 in the eastern province of Deir al-Zor on Sunday.
For Iran, preventing Assad’s fall is paramount; battling ISIS is of secondary importance.
Kerry added that such a move should not deter opposition groups trying to topple the Syrian government.
We urgently need to eliminate the sectarianism being spread by the Iranian regime.
U.S. Secretary of State John Kerry has said Syria is “weeks” away from a political transition.
France has called for a global alliance against Islamic State.