In September 1955, Aramburu participated in a military coup called the "Revolución Libertadora". He led the hardliners, and assumed the Presidency of Argentina himself, on November 13, 1955, after the resignation of moderate General Eduardo Lonardi. Admiral Isaac Rojas, was appointed Vice-President. The "Revolucion Libertadora", which overthrew Juan Domingo Perón, was triggered in part by the Perón's public confrontation with the Catholic Church over divorce laws, his actions towards the press as well as the imprisonment of opposition leaders and economic instability. The Revolución Libertadora led to three years of military rule under Aramburu, who allowed elections to be held in 1958 (won by Arturo Frondizi).

Aramburu's military government forced Perón into exile and barred the Peronist party from further elections. Known Peronists were persecuted and often imprisoned or murdered. Perón lived in exile in Spain until 1973 under the protection of Generalísimo Francisco Franco.

After the end of his presidential term in 1958, Aramburu retired from the military career and devoted himself entirely to politics. He ran for president in 1963, forming the "Union del Pueblo Argentino" (UDELPA, Union of the Argentine People), with the slogan: "Vote UDELPA and HE won't return" ("Vote UDELPA y no vuelve"), referring to Perón.

With the Peronists banned, the Presidential elections resulted in Arturo Umberto Illia becoming president, with Aramburu coming in third. Yet the military retained much real power, censoring both Peronism and its leader. The fragility of Argentine democracy was shown when Illia was overthrown in 1966 by a military coup led by General Juan Carlos Onganía.

In all those 15 years, Pedro Eugenio Aramburu was popular with much of the press. He often gave his opinions on society and politics (especially in Gente magazine, representative of Argentine high society). In 1970, he was mentioned as a possible Presidential candidate.

In 1960's, rumors about Perón's return to Argentina were circulated daily. From his exile in Spain, his voice grew stronger and stronger. At the same time, leftist strength grew in Argentina as in much of South America. The example of Che Guevara influenced a generation of students in schools and universities that supported international socialism. It was in this background that Montoneros, led by Mario Alberto Firmenich were formed. It is possible that the Montoneros would not have been really relevant had they not chosen to kidnap and kill Aramburu.

On May 29, 1970 at noon, Aramburu was snatched inside his apartment in Buenos Aires by two people posing as young army officers. Aramburu's disappearance kept Argentinian society on tenterhooks for a month, before it was discovered that Aramburu had been murdered three days after his kidnapping, and his corpse hidden inside a farmhouse near Timote, Carlos Tejedor, in Buenos Aires Province. He had been shot twice in the chest with two different pistols.

In the following weeks, statements from the Montoneros flooded the media. Among other things they claimed historical reasons for their actions such as "the execution of 27 Argentines after an unsuccessful Peronist rebellion in 1956", known as the José León Suárez massacre. The executions had been described by journalist and writer Rodolfo Walsh in his novel Operación Masacre.

In 1974, his body was stolen by Montoneros. The corpse was to be held until the President Isabel Peron brought back Evita Peron's body.