Numerous police officers led by the sheriff's department carried out the eviction with the aid of immigration and other officers.
Using a bullhorn, state attorney Kobus Meijer warned the migrants that they "will be arrested" and "detained" if they resisted removal.
Some families vacated voluntarily while others protested.
"It's better for me to die here" because "I am not going in Lindela" one refugee shouted.
The visibly distressed woman, with a dressing gown wrapped around her waist, is from the Democratic Republic of Congo.
UNHCR spokeswoman Laura Padoan told AFP that "they are asking that we transport them to a refugee camp in another country but this is outside of our mandate."
The UNHCR urged the evicting authorities to do so "peacefully and that families are treated humanely, with dignity and respect", said Padoan.
The scores of asylum-seekers began living in makeshift tents pitched outside the UNHCR offices asking to be relocated to other countries after a spate of xenophobic violence in 2019.
Pretoria municipality last week secured a high court order to remove them.
The court documents state that the refugees will be evicted and taken to the Lindela Repatriation Centre, a temporary holding center for undocumented migrants who are earmarked for deportation to their countries or origin.
South Africa boasts some of the world's most progressive asylum policies, allowing foreigners to apply for refugee status and work.
But rights groups say the application system is flawed and backlogged, leaving many asylum-seekers stuck in limbo for years.
South Africa is also a magnet for economic migrants - a situation that has stoked resentment among jobless South Africans and fueled sporadic outbursts of xenophobic violence.