However, during the talks, both sides agreed any polls must be well prepared.
The most revered man in Iraq for the country's majority Shia, al-Sistani has called for direct elections before US occupiers hand back sovereignty to Iraqis.
"Al-Sistani is insistent on holding the elections and we are with him on this 100% because elections are the best means to enable any people to set up a state that serves their interests," Lakhdar Brahimi said after holding two hours of talks with Sistani.
A UN team led by Brahimi is touring Iraq to assess the feasibility of holding early direct elections that Sistani has been urging in opposition to a US plan to choose a government by regional caucuses before handing over power by 30 June.
"We are in agreement with the Sayyid (al-Sistani) that these elections should be prepared well and should take place in the best possible conditions so that it would bring the results which the Sayyid wants and the people of Iraq and the UN,"
It was not clear if agreement on the need for preparations means al-Sistani may be flexible on his call for early elections.
The United States favours a gradual approach with caucuses that will eventually lead to direct elections in 2005.
Recent attacks on US troops and those who work with them could cast doubt on the practicality of early elections.
"Al-Sistani is insistent on holding the elections and we are with him on this 100%"
Brahimi, an Algerian, met the reclusive cleric in the holy city of Najaf accompanied by an Arab aide and Iraqi UN guards in Sistani's well-guarded complex.
The 73-year-old leader has not ventured out of his house or met a Westerner for years, aides say.
Al-Sistani, whose top religious rank grants him powerful influence in the Shia community, called mass demonstrations earlier this year to press for elections.
Brahimi is due to leave Iraq by Friday at the latest, a senior US-led administration official has said.
The rest of the UN team has started touring provinces. UN Secretary-General Kofi Annan is expected to give his opinion on the elections on 21 February.