UN Secretary General Ban Ki-moon said he accepted "with great regret" the resignation of Brahimi, who was appointed the Joint United Nations-League of Arab States Special Representative on the crisis in August 2012.
Brahimi took over the peace-facilitation role on the Syrian crisis from former UN Secretary-General Kofi Annan.
Dduring the daily press briefing here today, Ban said the 80-year old Algerian diplomat would relinquish his post as of May 31.
"For nearly two years, Joint Special Representative Brahimi has sought an end to the brutal and still worsening civil war in Syria. He has faced almost impossible odds, with a Syrian nation, Middle Eastern region and wider international community that have been hopelessly divided in their approaches to ending the conflict.
"He has persevered, with great patience and skill, because he knows that without efforts towards a new Syria, the Syrian people will be condemned to further suffering," Ban said.
Brahimi, present at the briefing, said he was "very, very sad to leave Syria in such a bad state".
Yet, he had no doubt the Secretary-General would do "everything humanly possible" to work with the UN Security Council, the Syrian parties and with neighbouring countries, to end the crisis.
"I'm sure the crisis will end, but all [stakeholders] should consider how much more death, how much more destruction will occur...Before Syria can become a new Syria," Brahimi added.
The conflict in Syria, which began in March 2011, has led to well over 100,000 deaths, and more than 680,000 people have been injured.
More than 9.3 million people are in need of assistance inside Syria, including at least 6.5 million who are internally displaced.
The conflict has also spawned a refugee crisis in which nearly 2.5 million people have are being sheltered in neighbouring countries, the UN said.
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