The high court's decision, which immediately canceled the prior ruling earlier on Tuesday, was handed down by Chief Justice Ricardo Lewandowski after a motion was presented by the Socialist Popular Party, or PPS.
The chief justice said that "the suspension of the service apparently violates the basic principle of freedom of expression and communication, enshrined in the Constitution, as well as prevailing legislation on the matter."
The high court's ruling is technically temporary, at least until the matter can be decided upon by the full court, and it came within the framework of a motion made by the PPS several months ago against the decision by another judge to block WhatsApp.
This was the third time in eight months that the messaging service had been temporarily blocked in Brazil on a judge's order, but in all three cases the halts were overturned by higher courts.
The PPS alleged in its motion that the judicial decisions against WhatsApp are "disproportionate" because they affect the right of consumers to freely communicate.
The initial court order blocking WhatsApp was relayed to all Brazilian telecommunications operators on Tuesday morning and went into effect at 11:30 a.m., the National Telecommunications Agency, or Anatel, reported.
The decision was handed by Judge Daniela Barbosa Assunção de Souza in the face of Facebook's refusal to reveal texts among people who are not being investigated for criminal activity.
The magistrate also had imposed a fine of 50,000 reais (about US$15,150) on Facebook for each day that it delays in turning over the requested information.
According to the judge, Facebook refused to abide by a judicial order after receiving three notifications to turn over to the courts copies of the messages exchanged between people who are not the targets of secret investigations.
De Souza added that Facebook said only that it does not save or copy the texts sent and received by WhatsApp users.
She also said that the service threatens public safety because many criminals no longer use telephones to communicate, but rather WhatsApp, because of the guarantee that the courts will not have access to their messages.
The app was blocked last December and again in May—affecting some 100 million Brazilian users of the service—by judges in different Brazilian cities but it returned to operation each time within 24 hours later via appeals court rulings.
Tech experts have said Facebook cannot comply with the Brazilian judges' demands because WhatsApp uses end-to-end encryption technology, preventing the company from monitoring texts traveling across its network.