"WhatsApp is blocked across the whole national territory," a spokesman for the court in Rio de Janeiro told AFP.
WhatsApp, owned by Facebook, has clashed several times with Brazilian courts after refusing to give access to police.
The 19-page ruling said that Brazilian telephone operators must "immediately suspend" WhatsApp services and also said that continued non-compliance would see the Facebook company fined 50,000 reais (USD 15,265) a day.
Shortly after the ruling was filed, WhatsApp messaging continued to function in Rio, however. It was not clear how quickly the order would be fulfilled.