The marchers, many belonging to Indonesia's conservative Prosperous Justice party (PKS), waved Palestinian flags and banners and collected donations on Sunday.
Others held banners with slogans such as: "Stop the embargo, save Palestine" and "One man, one dollar for Palestine."
"We voice protest against the US and Europe," Tifatul Sembiring, the PKS president, said in a speech at the Jakarta rally.
"They must revoke then ban because thousands of Palestinians are on the brink of famine."
The PKS also urged Indonesians to donate one dollar each to help fund the Palestinians.
The US and EU have both cut off direct financial aid for the Palestinian Authority after Hamas won in Palestinian elections earlier this year, demanding that Hamas renounce the armed struggle and recognise Israel.
Hamas has refused and in the ensuing financial crisis more than 165,000 government workers have not been paid for the past two months.
Smaller pro-Palestinian rallies were also held in major towns and cities across Indonesia.
Indonesia, the world's most populous Muslim country, is legally secular and religiously moderate, although the government has no formal relations with Israel.