President Hassan Rouhani attended but did not speak at the main rally in Tehran, which coincided with still seemingly deadlocked nuclear talks between Iran and world powers led by the United States.
In Iraq, thousands of people marched including hundreds of fighters in military uniform on Palestine Street in Baghdad to mark the annual day of solidarity inaugurated by the late Iranian revolutionary leader Ayatollah Ruhollah Khomeini.
In Lebanon, the leader of the powerful Shiite militia Hezbollah told thousands of supporters that Iran was the only hope of liberating the Palestinians.
The crowd in Tehran chanted "Down with US, Israel and the House of Saud", and carried placards that declared "Zionist soldiers kill Muslims" and "The Saudi family will fall".
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While the ongoing nuclear talks in Vienna are at the forefront of Iranian minds, they were only a backdrop to the procession in the capital.
Iran's relations with Saudi Arabia have sunk in the past six months since the Sunni kingdom began a bombing campaign against fellow Shiites in Yemen.
In Baghdad, protesters were mainly from Tehran-backed Shiite factions, including the powerful Badr, Ketaeb Hezbollah and Asaib Ahl al-Haq militias.
"We tell the enemies, as long as we have this mobilisation of young men, they will not be victorious," cleric Sheikh Khaled Mullah told the crowd.
"We ask God to bring back our Jerusalem and cleanse the land of Iraq from" IS, he said.
As is customary for Jerusalem Day, Israeli flags had been painted on the road for demonstrators to trample on.