The Danish foreign ministry said the ambassador and his colleagues temporarily left Damascus because their official protection had been reduced to an "unacceptably low level".
The German embassy will handle Denmark's consular interests until further notice.
This came as protesters from Nairobi to Kuala Lumpur, Istanbul to Islamabad, took to the streets after traditional Friday prayers.
However, there was no repeat of the violence that has so far left 13 people dead worldwide in demonstrations against cartoons first published by a Danish newspaper and reprinted by some other media in Europe.
Police in Egypt fired rubber bullets and tear gas at a crowd of about 12,000 people in the country's north, injuring 30.
In Nairobi, Kenyan security forces fired teargas at angry stone-throwing Muslim demonstrators attempting to march on the Danish embassy.
Baton-wielding riot police launched teargas canisters to disperse about 300 protesters who tried to storm a cordon by hurling rocks and other projectiles, witnesses said.
Thousands of people also demonstrated across Turkey, burning European flags and effigies of Danish Prime Minister Anders Fogh Rasmussen.
The largest demonstration was in the country's biggest city Istanbul where some 2,500 people gathered in front of the historic Beyazit mosque under heavy police presence.
Danish and US flags were also torched in demonstrations in Islamabad, while one protester was injured by a teargas canister at a rally in the northwestern city of Peshawar and smaller protests were held in Karachi, Lahore, Quetta and Multan.
Protesters in the Iranian capital Tehran threw petrol bombs at the French embassy and threw stones at the Danish and British missions, despite pleas by a senior cleric to stop the violence.
In his Friday prayer sermon, carried live on state radio, Hojatoleslam Ahmad Khatami also accused the United States of backing insults to Islam, and praised Muslim "holy rage" of the publication of the cartoons.
While he urged Muslims to continue their rage, he called for a halt to attacks on foreign embassies that have left some missions in flames.
Tens of thousands also marched in Bangladesh and India.
Newspapers have been censured in Indonesia and Malaysia for reprinting the cartoons.
Threats of further violence
Publication of the 12 cartoons by the Jyllands-Posten daily in September, but since reprinted in other nations and on the Internet, has stirred Muslim anger and raised questions about the limits of free speech.
In the Middle East, the radical group Islamic Jihad threatened to "burn the ground beneath the feet" of anyone who makes a future "attack" on the Prophet Mohammed.
"Apologies from European governments will do, but if they persist in their attack on the prophet we will burn the ground beneath their feet," said Jihad leader Khader Habib, during a rally in Gaza City attended by thousands.
"East-West chasm"
In Kuala Lumpur, where at least 1,000 protesters marched on the Danish embassy, Prime Minister Abdullah Ahmad Badawi warned that a huge chasm has opened up between the West and the Islamic world.
Speaking at an international conference in Kuala Lumpur, Mr Abdullah said Muslim fears of Western domination combined with the wars in Iraq and Afghanistan and the creation of Israel have provoked animosity between the two worlds.
"They think Osama bin Laden speaks for the religion and its followers. Islam and Muslims are linked to all that is negative and backward," said Mr Abdullah.
"The demonisation of Islam and the vilification of Muslims, there is no denying, is widespread within mainstream Western society," he said.
Mr Abdullah has promoted a more moderate form of Islam in Malaysia, which is relatively tolerant of religion despite being largely Muslim.
He has been an avid advocate of Muslims to embrace education, science, technology and development and shun extremism.
He urged both Muslims and the West to treat each other with greater respect and "accept one another as equals".