Khaled al-Ayoubi, who had been charge d'affaires, told the Foreign Office that he was unable to "represent a regime that has committed such violent and oppressive acts against its own people".
The most senior Syrian diplomat serving in London resigned on Monday, saying his conscience no longer allowed him to work for the regime of President Bashar al-Assad.
Khaled al-Ayoubi, who had been charge d'affaires, told the Foreign Office that he was unable to "represent a regime that has committed such violent and oppressive acts against its own people".
His departure was the latest in a series of diplomatic and military defections as the rebellion against Assad heads for its 18th month and the death toll approaches 19,000 by some estimates.
Ayoubi, an ethnic Kurd who joined the Syrian diplomatic service in 2001, was understood to be in discussion with British officials last night. He was said to be considering his next move at a safe location with his immediate family.
He was not available for comment, but the Foreign Office hailed his departure as "another blow to the Assad regime".
It said: "It illustrates the revulsion and despair the regime's actions are provoking amongst Syrians from all walks of life, inside the country and abroad.
"We urge others around Bashar Al-Assad to follow al-Ayoubi's example; to disassociate themselves from the crimes being committed against the Syrian people and to support a peaceful and free future for Syria."
Ayoubi's decision has not been described as a defection because he has yet to switch his allegiance to Syrian opposition groups, though it will be regarded as such in Damascus.
Having arrived in London as second secretary in February 2011, he leaves just five Syrians of more junior rank behind him at the London embassy in Belgrave Square.
Three colleagues including his predecessor as charge d'affaires were kicked out in May as part of a coordinated series of expulsions by the West in response to a massacre committed by Syrian forces in Houla.
Assad withdrew his ambassador, Sami al-Khiyami, in March after Britain, the United States and several European countries closed their embassies in Damascus because of security concerns. The only European embassy still open in Damascus is that of Hungary.
Recent weeks have seen a surge in defections and resignations as fighting has intensified in the country's major cities. They have included Nawaf Fares, the ambassador to Iraq, and Manaf Tlas, a friend of Assad and former brigadier general in the Republican Guard.
The deputy police chief in Latakia was among 12 officers who reportedly fled across the border to Turkey early yesterday. The city on the Mediterranean coast is dominated by members of Assad's Alawaite sect and has been mooted as a possible refuge for the president.
Syria also closed its embassy in Australia amid reports that some of its staff were seeking asylum.
Meanwhile, France has promised to revive the effort to apply diplomatic pressure on Damascus at the United Nations. Laurent Fabius, the French foreign minister, said that he would call an emergency ministerial meeting on Syria when his country takes over the United Nations Security Council's rotating presidency tomorrow.
Fabius said: "We must try everything" even though Russia and China have blocked three resolutions on Syria.
"We cannot say that it is a domestic matter," he added, warning that the conflict could spread into neighbouring countries.
"The Syrian people are being martyred and the executioner is called Bashar Al-Assad," he said.
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