Videos and photos from the demonstration show about 200 protesters throwing rocks, breaking down barriers, and waving flags as the fire raged on the Mexico City embassy.
Riot police stood in front of the masked protesters and deployed tear gas into the crowd, Al Jazeera reported.
Security forces had created a barricade preventing access to the Israeli embassy in Mexico City's Lomas de Chapultepec neighborhood.
At least six people were injured in the chaos, including several journalists, according to unverified reports.
Comment:
The "Urgent Action for Rafah" demonstration occurred after an Israeli attack on Sunday on a displacement camp outside Rafah, which killed 45 people, according to Palestinian officials.
Comment: Israel admitted the bombing and said it would 'investigate' itself.
The riot also came after Mexico filed a declaration of intervention in South Africa's "genocide" case against Israel at the International Court of Justice (ICJ).
The ICJ issued a ruling on Friday that Israel must "immediately halt its military offensive and any other action in the Rafah governorate, which may inflict on the Palestinian group in Gaza conditions of life that could bring about its physical destruction in whole or in part."
Israeli Defense Minister Yoav Gallant said on Sunday that the IDF would continue to press its offensive in Rafah in order to free the Israeli hostages held by Hamas.
Officials in Israel have also insisted that the military operations occurring in Rafah are in conformity with the ICJ's ruling.
Similar protests to the one in Mexico erupted around the world following Sunday night's Israeli attack on Rafah, which is considered a safe zone.
Comment: Even Western mainstream commentators are acknowledging that Israel's crimes against humanity are turning it into a pariah state: Istanbul protesters set fire to vicinity of Israeli consulate following Rafah massacre