Assad reportedly signed a decree removing Ahmad Khaled Abdel Aziz, following some of the biggest demonstrations yet against his rule.
The Syrian Observatory for Human Rights described protests in Hama, where tens of thousands of people took to the streets, as “the biggest demonstration since the Syrian revolution broke out”.
BBC correspondents said they had reports the army had eased its presence in Hama earlier in the week.
A local activist confirmed to Al Jazeera that there was no visible security presence in Hama, only checkpoints at the entrances. “There's not even traffic police,” he said.
In 1982, the Syrian army crushed a Muslim Brotherhood uprising against Assad's father, Hafez, killing at least 10,000 people.
Across the rest of the nation Friday, hundreds of thousands took to the streets, with human rights groups saying that at least 24 people had been killed by security forces.
Al Jazeera reported from the Syrian capital Damascus, Saturday, that over the past three months, a young leadership has emerged from the protests, which was looking to organise itself into committees.
“At different levels you have people, the opposition figures ... and famous people who have been battling the regime for years,” said the network's correspondent, Rula Amin.
Activists say more than 1,350 civilians and 350 security personnel have been killed in Syria since protests began in mid-March.