Bush is scheduled to spend a few hours in the world's largest Muslim nation on Monday on his way home from the Asia Pacific Economic Cooperation (APEC) summit in Hanoi.
Muslim political groups and some religious leaders have condemned the visit and President Susilo Bambang Yudhoyono for inviting the US leader.
Addressing some 7,000 people in front of the presidential Merdeka Palace, Habib Rizqie, the head of the militant Front for the Defenders of Islam, said that the deaths of Muslims across the globe should be revenged.
"His blood is Halal (permitted under Islam) to be shed. Not only is it halal, but it is obligatory to kill him," Rizieq told the crowd.
"Kill, kill" the crowd yelled, pointing their fists up, when Rizieq shouted Bush's name, while the shouting of "America" was greeted with shouts of "Destroy, destroy."
Hundreds of policemen were lined up behind a barbed wire barricade preventing the protestors from getting close to the palace.
Speakers, all calling Bush the devil and condemning the visit, also warned Indonesian President Susilo Bambang Yudhoyono and Vice President Yusuf Kalla, that they risked election defeat for receiving Bush.
"SBY (Susilo Bambang Yudhoyono) step down from the throne if you cannot uphold the dignity of the nation," said a large poster while a man was holding a picture of a young Osama bin Laden with the words: "Want to go to heaven? Kill Bush."
Bush is scheduled to spend most of his visit at the Summer Palace in the resort town of Bogor.
Safiatun, 36, who came to the Jakarta protest with her two young children and a group of other veiled women from nearby Depok, said they had come to show support for the anti-Bush drive.
"I just hate Bush," she said, adding the standard motto of the day, that "Bush is the devil."
The rally was organised by the Muslim Forum, an umbrella organisation grouping some 80 Islamic groups -- mostly conservatives.
At another protest in south Jakarta, more than 5,000 supporters of the Islamic political party PKS (the Prosperous Justice Party) rallied against the visit on the grounds of a mosque.
PKS head Tifatul Sembiring later blessed representatives of some 2,000 party members who were to leave for Bogor to join a major planned protest rally there Monday.
Besides the hundreds of police guarding the main rally at the palace, at least six trucks and six buses full of police were deployed to guard a roundabout popular with protesters.
ElShinta radio also reported massive protests against the visit, involving more than 1,000 Muslims in Makassar, South Sulawesi and in Surabaya, East Java, while smaller protests were also reported in at least eight other cities in Sumatra and Jva.
The US president's brief visit to Indonesia has triggered daily street demonstrations and a threat to move a no-confidence motion against Yudhoyono.

Copyright AFP (Agence France-Presse), 2006