The group later tore down and burned the country's white and red flag.
The rowdy protest by about 70 people was one of the first in the world's most populous Muslim nation against the 12 cartoons, which first appeared in September in a Danish newspaper. They were reprinted in several other European newspapers this week in a gesture of press freedom.
"We are not terrorists, we are not anarchists but we are against those people who blaspheme Islam," one of the protesters shouted outside the building, which also houses several other foreign missions in Jakarta.
They pelted the building with eggs, pushed their way past security guards and milled around in the lobby before leaving of their own accord after five minutes. They then tore the embassy's flag down from outside the building and lit it on fire on the pavement.
The demonstrators also stopped outside an Indonesian newspaper which briefly ran one of the cartoons on its Web site Thursday to illustrate its story on the uproar generated by them elsewhere in the Muslim world.
Editors of Rakyat Merdeka met some of the protesters, but it was not known what they told them.
Pakistan's parliament passed unanimously a resolution Friday condemning cartoons of Islam's prophet in European newspapers, and small protests were held in major cities as anger grew in this Islamic nation.
Pakistani President Gen. Pervez Musharraf also expressed outrage, saying the cartoon couldn't be justified as freedom of expression.
Also Friday, about 500 Muslims rallied in Bangladesh's capital of Dhaka. Many devotees spontaneously joined the protest rally held downtown outside the country's main mosque after weekly prayers in the afternoon. No violence was immediately reported, said a Dhaka Metropolitan police official on condition of anonymity.
On Thursday, Palestinian gunmen briefly kidnapping a German citizen and protesters in Pakistan chanting "death to France" and "death to Denmark."
Islamic tradition bars any depiction of the prophet, favorable or otherwise, to prevent idolatry. The drawings have prompted boycotts of Danish goods, bomb threats and demonstrations against Danish facilities in Muslim nations.
Indonesia's government reiterated earlier criticism of the paper's decision to publish.
"This is about insensitivity and a trend toward Islamaphobia," said foreign ministry spokesman Yuri Thamrin. "As a democratic country we are very aware of press freedom, but we also believe it should not be used to slander, or defame sacred religious symbols."
Palestinian militants surrounded European Union headquarters in Gaza, and gunmen burst into several hotels and apartments in the West Bank in search of foreigners to take hostage.
In Iraq, Islamic leaders urged worshippers to stage demonstrations from Baghdad to the southern city of Basra following weekly prayer services Friday. Afghanistan and Indonesia condemned the drawings, and Iran summoned the Austrian ambassador, whose country holds the EU presidency.
The issue opened divisions among European Union governments. Austrian Foreign Minister Ursula Plassnik said EU leaders have a responsibility to "clearly condemn" insults to any religion. But French Interior Minister Nicolas Sarkozy said he preferred "an excess of caricature to an excess of censorship."
Sarkozy joined journalists in rallying around the editorial director of France Soir, who was fired by the newspaper's Egyptian owner. France Soir and several other newspapers across Europe reprinted the caricatures this week in a show of support for freedom of expression.
The cartoons were first published in September in a Danish newspaper, touching off anger among Muslims who knew about it. The issueafter Saudi Arabia recalled its ambassador to Denmark. When the cartoons were first published five months ago, though, the controversy was low-key, CBS News correspondent Richard Roth reports. Boycotts were called against Danish goods in the Middle East. But the anger spread fast.
The Danish newspaper, Jyllands-Posten, had asked 40 cartoonists to draw images of the prophet. The purpose, its chief editor said, was "to examine whether people would succumb to self-censorship, as we have seen in other cases when it comes to Muslim issues."
Critics say the drawings were particularly insulting because some appeared to ridicule Muhammad. One cartoon showed the prophet wearing a turban shaped as a bomb.
France's Grand Rabbi Joseph Sitruk said he shared Muslim anger.
"We gain nothing by lowering religions, humiliating them and making caricatures of them. It's a lack of honesty and respect," he said. He said freedom of expression "is not a right without limits."
In the Arab world, a Jordanian newspaper, Shihan, took the bold step Thursday of running some of the drawings, saying it wanted to show its readers how offensive the cartoons were but also urging the world's Muslims to "be reasonable." Its editorial noted that Jyllands-Posten had apologized, "but for some reason, nobody in the Muslim world wants to hear the apology."
"We're living in a political climate where governments and the media in the West feel they can get away with something like this," Anjem Choudary of the British Society of Muslim Lawyers told Roth. "There are double-standards here. I think you need to appreciate the Muslims take their religion very seriously."
Hours later, the Jordanian government threatened legal action against Shihan, and the owners of the weekly said they had fired its chief editor, Jihad al-Momani, and withdrawn the issue from sale.
Palestinian security officials said they would try to protect foreigners in Gaza. Nineteen foreigners have been kidnapped in Gaza in recent months; all were freed unharmed.
In one unusual twist, Mahmoud Zahar, a Hamas leader, visited a Gaza church Thursday and promised protection to Christians after Fatah gunmen threatened to target churches as part of their protests. Zahar offered to dispatch gunmen from Hamas' military wing, the Izzedine al Qassam Brigades, to guard the church.
"You are our brothers," Zahar told Father Manuel Musallam of the Holy Family Church.