The kingdom handled last year's haj visa applications without cooperating with Damascus.
But Riyadh has now decided that the opposition council is "entitled to issue haj permits for the Syrians," haj ministry spokesman Hatem Qadi told AFP.
He said Saudi authorities took the decision after a coalition delegation visited the haj ministry.
This year's pilgrimage falls in October.
The move shows the kingdom's eagerness to give further legitimacy to Syria's opposition.
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But Saudi Arabia rejected the accusation, saying King Abdullah ordered consulates in countries neighbouring Syria to facilitate visas for Syrians wishing to perform the haj.
The pilgrimage is one of the five pillars of Islam and must be performed at least once in a lifetime by those who are able to make the journey to Mecca.
Every Muslim country has a haj quota of 1,000 pilgrims per million inhabitants.
Like many Arab countries, Saudi Arabia has cut ties with Syria's government and called on President Bashar al-Assad to leave power.