Amidst growing workers' and students' unrest, another coup took place in June 1966, self-designated Revolución Argentina (Argentiene Revolution), which established General Juan Carlos Onganía as de facto president, supported by several leaders of the General Confederation of Labour (CGT), among whom the general secretary Augusto Vandor. This led to a series of military-appointed presidents.
While preceding military coups were aimed at establishing temporary, transitional juntas, the Revolución Argentina headed by Onganía aimed at establishing a new political and social order, opposed both to liberal democracy and Communism, which gave to the Armed Forces of Argentina a leading, political role in the economic rationalization of the country. The political scientist Guillermo O'Donnell named this type of regime "authoritarian-bureaucratic state", in reference both to the Revolución Argentina, the Brazilian military regime (1964–1985), Augusto Pinochet's regime (starting in 1973) and Juan María Bordaberry's regime in Uruguay.
Onganía's Minister of Economy, Adalbert Krieger Vasena, decreed a freeze of wages' increase and a 40% devaluation, which strongly affected the state of the Argentine economy, in particular of the agricultural sector, favoring foreign capital. Vasena suspended collective labour conventions, reformed the hydrocarburs law which had established a partial monopoly of the Yacimientos Petrolíferos Fiscales (YPF) state enterprise, as well as passing a law facilitating expulsions in case of fault of payment of rent. Finally, the right to strike was suspended (Law 16,936) and several other laws reversed progress made concerning labor laws through-out the preceding years.
The workers' movement divided itself between Vandoristas, who supported a "Peronism without Peron" line (Vandor declared that "to save Perón, one has to be against Perón") and advocated negotiation with the junta, and Peronists, themselves divided.
In July 1966, Onganía ordered the forcible clearing of five facilities of the Universidad de Buenos Aires (UBA) in Argentina on July 29, 1966 by the Federal Police, an event known as La Noche de los Bastones Largos ("The Night of the Long Police Sticks"). These facilities had been occupied by students, professors and graduates (members of the autonomous government of the university) who opposed the military government's intervention in the universities and revocation of the 1918 university reform. The university repression led to the exile of 301 university professors, including Manuel Sadosky, Tulio Halperín Donghi, Sergio Bagú and Risieri Frondizi.
In late May 1968, General Julio Alsogaray dissented from Onganía, and rumors spread about a possible coup d'état, Algosaray leading the conservative opposition to Onganía. Finally, at the end of the month, Onganía dismissed the leaders of the Armed Forces: Alejandro Lanusse replaced Julio Alsogaray, Pedro Gnavi replaced Benigno Varela, and Jorge Martínez Zuviría replaced Adolfo Alvarez.
On 19 September 1968, two important events affected Revolutionary Peronism. On one hand, John William Cooke, former personal delegate of Perón and ideologist of the Peronist Left, as well as a friend of Fidel Castro, died from natural causes. On the other hand, a small group (13 men and one woman) who aimed at establishing a foco in Tucuman Province, in order to head the resistance against the junta, was captured. Among them was Envar El Kadre, then a leader of the Peronist Youth.
In 1969, the CGT de los Argentinos (CGTA, headed by the graphist Raimundo Ongaro) headed social movements, in particular the Cordobazo, as well as other movements in Tucuman and Santa Fe. While Perón managed a reconciliation with Augusto Vandor, head of the CGT Azopardo, he followed, in particular through the voice of his delegate Jorge Paladino, a cautious line of opposition to the military junta, criticizing with moderation the neoliberal policies of the junta but waiting for discontent inside the government ("hay que desencillar hasta que aclare", said Perón, advocating patience). Thus, Onganía had an interview with 46 CGT delegates, among whom Vandor, who agreed on "participationism" with the military junta, thus uniting themselves with the Nueva Corriente de Opinión headed by José Alonso and Rogelio Coria.
In December 1969, more than 20 priests, members of the Movimiento de Sacerdotes para el Tercer Mundo (MSTM, Movement of Priests for the Third World), marched on the Casa Rosada to present to Onganía a petition pleading him to abandon the eradication plan of villas miserias (shanty towns).
Meanwhile, Onganía implemented corporatism policies, experimenting in particular in Córdoba, underneath Carlos Caballero's governance. The same year, the Movement of Priests for the Third World issued a declaration supporting Socialist revolutionary movements, which lead to the Catholic hierarchy, by the voice of Juan Carlos Aramburu, coadjutor archbishop of Buenos Aires, to proscribe priests from making political or social declarations.