The court orders the Trump administration not to deport the Venezuelans "until further decisions are made in court". Two of the nine judges in the conservatively dominated court reserved themselves.
Behind the decision lies an appeal by the organization American Civil Liberties Union (ACLU), which claims that the immigration authorities are attempting to resume deportations based on a war law from 1798.
"We are very relieved that the court has temporarily stopped the deportations. These individuals were in immediate danger of spending the rest of their lives in a brutal Salvadoran prison without ever having received a fair trial", says a lawyer at ACLU in a statement.
The Supreme Court decided earlier in April that the deportations could only continue if those affected have a "reasonable time" to seek a legal review before being deported.
The deportations to El Salvador of migrants allegedly being gang members have received significant attention. The Supreme Court has ruled that the government must bring home a Salvadoran migrant who was mistakenly deported. However, the Trump administration has not complied with the request.