As President of the Supreme Federal Court, he was called by the Armed Forces to take over the Presidency following the ousting of Getúlio Vargas in 1945, to the inauguration of Eurico Gaspar Dutra, in 1946, which marked the beginning of what is known today as the Fourth Brazilian Republic.

Linhares devoted himself mainly to prepare the return to democratic order, replacing the stakeholders in the states by judiciary members, giving the new parliament constitution-making powers, extinguishing the Court of National Security, abolishing the state of emergency, provided in the 1937 Constitution, among other measures.

In the economic and administrative field, acted against inflation, revoked the antitrust law, one of the factors that led to the deposition of Vargas, and extinguished the Council of People's Economy.

Granted autonomy to the University of Brazil and regulated various departments of the Ministry of Transportation and Public Works.

José Linhares remained in office until the inauguration of the elected president, Eurico Gaspar Dutra.