The Jerusalem District Court Thursday made the ruling, overturning a previous decision barring the deportation after a number of non-government organizations argued the migrants would be in grave danger if they returned home, The Jerusalem Post said.
Interior Minister Eli Yishai praised the ruling, saying he hoped it would be the first step in the expulsion of the entire migrant population.
"I praise the court decision that will pave the way for the expulsion of around 1,500 infiltrators from South Sudan. I hope this is just the first of many steps that will allow us to expel the infiltrators from Eritrea and Sudan as well," the paper quoted Yishai as saying.
The Israeli minister described the situation as a "a war for the preservation of the Zionist and Jewish dream in the land of Israel."
Thousands of migrants from Sudan and Eritrea have infiltrated into Israel via the porous Egyptian border, settling in southern Tel Aviv neighborhoods. Their presence has generated severe racial tensions and violent demonstrations by local residents.