The encounter came a day after the Red Crescent evacuated hundreds of civilians from a besieged town near Damascus, in an operation that saw rare cooperation among the regime, its opponents and the international community.
Brahimi has been travelling the Middle East since mid-October to muster support for proposed peace talks dubbed Geneva II.
On Thursday he is due to meet opposition members in Damascus tolerated by the regime and travel to Lebanon the following day.
The Syrian leg of the tour is the most sensitive, as the veteran Algerian diplomat needs to persuade a wary regime and an increasingly divided opposition to attend.
During his last visit to Damascus in December, Brahimi was heavily criticised by Syrian media for asking Assad if he intended to step down at the end of his presidential term in mid-2014.
Wednesday's meeting with Assad lasted less than one hour, and the president criticised foreign interference in his country.
"The Syrian people are the only ones who have the right to decide on Syria's future," state media quoted Assad as telling Brahimi.
"Putting an end to support for the terrorists and pressuring the states that support them is the most important step to prepare... for dialogue," he said, using his regime's term for rebels.
"The success of any political solution is linked to putting an end to support funnelled to terrorist groups."
Brahimi's spokeswoman earlier said he hoped Saudi Arabia, a main backer of the rebels, would take part in the proposed talks.
State television reported that Brahimi agreed with Assad that Syrians themselves need to find a solution to the conflict that has been ravaging the country since March 2011.
In an interview this month, Assad cast doubt on the possibility of his regime attending, saying he would not negotiate with any group tied to the rebels or to foreign states.
The main opposition National Coalition has said it will refuse to take part in any talks unless Assad's resignation is on the table, and some rebel groups have warned participants will be considered traitors.
Meanwhile. Russian Foreign Minister Sergei Lavrov, whose country is a key backer of the Assad regime, blasted critics of the talks.
"Open objections have surfaced against holding this Russia-US meeting, not only among Syrian sides but also among capitals, both in neighbouring and non-neighbouring states," Lavrov said in Athens.
"We must not allow this initiative to fizzle out," he added.
In an interview with Russian business daily Kommersant French Prime Minister Jean-Marc Ayrault said everything should be done to make the planned Geneva talks a success that will usher in a transition government.
Speaking ahead of his visit Thursday to Moscow, Ayrault said he was "pleased that Russia took the initiative" to push for the dismantling of Syria's chemical weapons arsenal.
"The objective now is to make Geneva II a success," said Ayrault. "This implies that conditions are created that the Syrian National Coalition can take part in it and that the conference leads to a transitional government wielding full executive powers including the presidency."
More than 115,000 people have been killed in the 31-month armed uprising against the Assad regime triggered by his forces' bloody crackdown on Arab Spring-inspired democracy protests.
Thousands still trapped in besieged town
The war has also triggered a massive humanitarian crisis, with millions of people displaced internally and more than two million who fled the spiralling violence.
On Tuesday, some 800 women, children and elderly civilians were evacuated from Moadamiyet al-Sham, said Wassim al-Ahmad of the council in the town southwest of Damascus.
But Ahmad said around 6,000 civilians remained trapped.
Television footage showed the evacuees clutching a few personal belongings as they streamed out of the town along a dusty road, with Red Crescent staff carrying an elderly man and assisting another too frail to walk.
"All sides, without exception, took part (in the evacuation), including the opposition as represented by the National Coalition, the regime... and the international community," an opposition activist said.
Widespread malnutrition has been reported in Moadamiyet al-Sham, especially among children, because of an almost year-long army siege that has blockaded the entry of food and other vital goods.
The town was the scene of one of the sarin gas attacks in August that killed hundreds of people.
Meanwhile, the World Health Organisation confirmed 10 polio cases in the northeastern province of Deir Ezzor, all of them in children under the age of two.
On the ground, violence as six people were killed in army shelling of southern Damascus and 11 others in a rebel attack in central Syria, a monitoring group said.