The demonstration capped a two-day march by the migrants, who fled a detention center in southern Israel on Sunday and made their way to Jerusalem to draw attention to their plight.
They want the government to end the detentions and recognise them as refugees.
"We're talking about people who have nothing to lose," said Michal Rotem, an Israeli activist who took part in the march. "This is their last chance to come and say... We want our freedom."
The migrants are allowed to leave the facility but are required to report back three times a day and may remain there indefinitely. Some 500 migrants now reside in the new facility. Critics say the policy is an attempt to prod the migrants to leave Israel.
The Africans say they are fleeing hardship and danger in their native countries. Israel says they are economic migrants looking for work.
"We come here to ask for protection. We don't want to go back to our country," said Brahani Beraki, a 29-year-old from Eritrea, whose government is widely accused of torture, restrictions on freedom of expression and other human rights violations. "Our country is a bad situation ... We need to save our life here."
Police spokesman Micky Rosenfeld said some 180 people were detained and the area was cleared out. He said they were expected to be returned to detention facilities in the southern desert. No injuries were reported.
The symbolic march began Sunday when about 150 migrants left Holot to make the two-day trip on foot and by bus to Jerusalem.
Israel has attempted to ebb the flow of African migrants, who come mainly from Sudan and Eritrea and now number about 53,000.
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