A statement from police said that hundreds were arrested in Riyadh’s Manfuhah neighborhood.
On different social media sites, video showed the government security forces wearing riot gear and using truncheons to scatter the largest groups of protesters.
Police last week rounded up migrant workers by the thousands after the amnesty that had been linked to employment rules had expired.
On Saturday, police announced they had intervened after the foreign workers in Manfuhah rioted and attacked Saudi as well as foreign residents with knives and rocks.
The neighborhood of Manfuhah has many migrants with the majority from east Africa. One of those killed was from Saudi Arabia, while the other still had not been identified, said police. Nearly 70 others had been injured, while more than 560 had been arrested, said officials.
Witnesses said on Sunday that police had surrounded the area while National Guard units and other special forces had been sent in.
Hundreds of men, woman and children nearby were lined up with their belongings preparing to boards buses supplied by the police to transport them to a center where they will stay prior to being deported.
Other migrant workers could be seen leaving Manfuhah in taxis.
Last Monday, authorities started rounding up illegal foreign migrant workers by the thousands following the expirations of their amnesty of seven months that gave them time to formalize their legal status.
On Wednesday, a man from Ethiopia was reported killed, as police in Saudi started transporting the illegal immigrants into camps.
The Addis Ababa government said it would provide support to the workers and would help to repatriate its people.
Close to one million Indians, Filipinos, Bangladeshis, Pakistanis, Yemenis and Nepalese are believed to have left Saudi Arabia over the last 90 days.
Four million more obtained permits to work prior to the deadline of last Sunday.
Saudi Arab has the largest economy in the Arab world but authorities there are trying to lower the unemployment rate of 12% amongst native Saudis.
Close to nine million workers from other countries, live in Saudi Arabia.