Authorities with loudspeakers warned the protesters to maintain social distancing.
More than 2,300 police, many wearing hazmat suits, were deployed to secure the embassy, the nearby presidential palace and the United Nations mission.
Indonesia, the world's most populous Muslim-majority nation, does not have formal diplomatic relations with Israel and has long been a strong supporter of Palestinians.
Indonesian President Joko Widodo has condemned the deadly Israeli airstrikes on the blockaded Gaza Strip.
A cease-fire took effect last week.
