Brahimi, who travelled overland to the Syrian capital after flying in to Beirut airport from Tehran, arrived at the Sheraton hotel accompanied by Syrian deputy foreign minister Faisal Moqdad.
The envoy has been on a regional tour, taking in Turkey but not Saudi Arabia which opposes the peace initiative and takes a hard line against President Bashar al-Assad's regime.
The Syria leg of his mission to drum up support for Geneva II is the most sensitive as he needs to persuade a wary regime and its hostile opponents to attend the talks.
In Tehran, Brahimi said it was "necessary" for Iran, a key ally of the Damascus regime, to take part in the Geneva conference slated for next month and aimed at ending Syria's two-and-a-half-year conflict.
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The initiative's backers, Washington and Moscow, have struggled to win the support of the warring parties in Syria, where more than 115,000 people are estimated to have been killed in the 31-month conflict.
In the latest blow, 19 Islamist groups fighting to topple Assad issued a statement on Sunday saying the Geneva conference "is not, nor will it ever be our people's choice or our revolution's demand."
The statement went on to say that anyone who attends such talks would be committing "treason" and "would have to answer for it before our courts," implying they could face execution.
Russia today issued a stinging rebuke to the rebels.
"It is outrageous that some of these extremist, terrorist organisations fighting government forces in Syria are starting to make threats," Foreign Minister Sergei Lavrov said in televised comments.
For Thierry Pierret, an expert on Islam in Syria, the rebel statement covers a wide range of opposition groups from radical Salafists to moderates who form the backbone of the mainstream rebel Free Syrian Army.
"So you can say that Geneva II is almost totally rejected within rebel ranks," said the expert at Scotland's Edinburgh University. "If some of the opposition does take part and reaches an accord, it will be worthless.