Mr Brahimi said they discussed “many steps to be taken in the future”, but he did not elaborate.
On Sunday, opposition activists said dozens of people had been killed in a government air strike in the rebel-held town of Halfaya in Hama province.
Syrian state media blamed a “terrorist group” for the attack.
Mr Brahimi drove into Syria from Beirut on Sunday, after fighting closed Damascus airport.
“I had the honour to meet the president and as usual we exchanged views on the many steps to be taken in the future,” he said after meeting President Bashar al-Assad on Monday.
President Assad expressed support for “any effort in the interest of the Syrian people which preserves the homeland’s sovereignty and independence”, the state-run Sana news agency reports.
It is the third visit to Damascus by Mr Brahimi since he was appointed joint UN-Arab League envoy to Syria in August.
However, he has made little progress on a peace process so far and it is unclear what new ideas he may be bringing.
Rebels have been fighting Mr Assad’s government for 21 months. Opposition groups say more than 44,000 people have been killed.
In the latest violence, activists said a government air strike had struck a bakery in Halfaya on Sunday.
They put the number of dead at more than 90, but the BBC’s Jim Muir in neighbouring Lebanon says they named or otherwise identified only 23 of them – all men.
One activist in Halfaya, Samer al-Hamawi, told Reuters news agency: “There is no way to really know yet how many people were killed. When I got there, I could see piles of bodies all over the ground.
“We hadn’t received flour in around three days so everyone was going to the bakery today, and lots of them were women and children. I still don’t know yet if my relatives are among the dead.”
Syrian state TV blamed an “armed terrorist group” for the attack, saying the group had then filmed the incident to blame it on government troops.
Five days ago, the rebel Free Syrian Army declared Halfaya a “liberated area” after taking over army positions there.
Our correspondent says the rebels want to take control of the whole of Hama and link up the territory they control.
As has happened many times before, he adds, the government has hit back with massive firepower at the areas it has lost.
A UK-based activist group, the Syrian Observatory for Human Rights (SOHR), said there had been other air strikes on Sunday, including one on the town of Safira in northern Aleppo province, which killed 13 people.
It said more than 180 people had been killed across the country on Sunday.
The SOHR is one of the most prominent organisations documenting and reporting incidents and casualties in the Syrian conflict. The group says its reports are impartial, though its information cannot be independently verified.