Judge Julier Sebastiao da Silva was reacting to US plans to do the same to Brazilians entering the United States.
He made the order after a Brazilian government office filed a complaint in a federal court over the new US immigration measures.
From 5 January, travellers from all countries which need a visa to enter the US will undergo the same checks.
"I consider the act absolutely brutal, threatening human rights, violating human dignity, xenophobic and worthy of the worst horrors committed by the Nazis," Federal Judge Julier Sebastiao da Silva said in the court order.
The new security measures will come into effect on 1 January unless Mr Da Silva's ruling is challenged by the justice system.
More at: http://news.bbc.co.uk/1/hi/world/americas/3358627.stm
Steven