Moríñigo was born in Paraguari, Paraguay in 1897, the son of a merchant. Little is known of his early life, though he served in the Army in the Chaco War and served as Chief of Staff for President Rafael Franco (1936-39). Of European and Guarani descent, He was fluent in both the Spanish and Guarani languages. Franco's successor, José Félix Estigarribia of the Liberal Party, appointed Moríñigo as his Minister of War on May 2, 1940. Four months later, President Estigarribia was killed in an airplane crash on September 7, 1940, and the cabinet selected General Moríñigo to serve as President for two months until elections could be held .
On September 30, the Liberal Party ministers in his cabinet resigned, and on October 16, Moríñigo announced that the presidential elections would be postponed for two years. Soon afterward, he announced a policy of "disciplina, jerarquia, y orden" (discipline, hierarchy, and order) and stated that persons who spread subversive ideas would be "subject to confinement" . On November 30, he announced in a noontime radio address that "The people and the Army, from this moment, will be under a single command." All political parties were banned. Moríñigo organized the Guion Rojo (the "Red Banner") as a state police force to control dissent from the Febreristas and the Liberals, and exiled opposition newspaper publishers. . The elections took place as promised on February 15 1943. However, Moríñigo was the sole candidate on the ballot.
Moríñigo's absolute rule lasted until June 9, 1946, when he formed a cabinet with the Revolutionary Febrerista Party and the Colorado Party. During his dictatorship, Moríñigo faced widespread resistance, including general strikes, but he survived by maintaining the loyalty of the Paraguayan Army, which received 45% of the country's budget.
Feeling that Moríñigo was favouring the Colorados, the Febreristas resigned and made common cause with the Liberal Party and the Communist Party of Paraguay in the Paraguayan Civil War of 1947. Although large sections of the military defected to the rebels, Moríñigo regained control of the country by the end of the year, with the assistance of grass-root militias organized by the Colorados. For the next 15 years, the Colorados were the only legal party in Paraguay. Moríñigo permitted a presidential election in 1948, and on February 15 of that year, Colorado Party candidate Juan Natalicio González was elected as the only candidate on the ballot. Moríñigo's term was to expire on August 15, but revolution was threatened by groups dissatisfied with González. The Paraguayan Army deposed Moríñigo on June 3, about two months ahead of schedule. Supreme Court Chief Justice Juan Manuel Frutos was sworn in as interim president, serving until González was inaugurated on August 15, 1948. .