The blatancy of the fraud employed to maintain the PCN [National Conciliation Party (Partido de Conciliacion Nacional--PCN)] in power outraged and disillusioned many Salvadorans, including members of the armed forces. One faction of the officer corps, a new Military Youth, attempted to take direct action to redress the official exploitation of a system that had until that point shown some promise of evolving in a genuinely democratic direction. This group of young army officers, led by Colonel Benjamin Mejia, launched a coup on March 25, 1972. Their immediate goal was the establishment of a "revolutionary junta." It seemed clear, however, that the officers favored the installation of Duarte as president.

Mejia and his followers initiated their action by seizing the presidential residence and taking Sanchez and some of his family members hostage. From that point on, however, events ran against the insurgents. The thunder of aerial bombing over the capital soon announced the loyalty of the air force to the government. The coup attempt never gained the support of more than a minority within the officer corps, and that only in the army. Some residents of the capital took to the streets in support of the young officers, but they were no match for the loyalist military forces. In desperation, Mejia turned to Duarte, urging him to deliver a radio address in support of the rebels. Despite some misgivings, Duarte agreed. His address was broadcast shortly after noon and may have saved some lives by warning civilians to evacuate areas targeted for rebel artillery strikes. Its overall impact, however, was insufficient to reverse the tide of action in the streets. Loyalist forces regained effective control of San Salvador by early that evening.

Like many other government opponents, Duarte sought refuge within the foreign diplomatic community. He was taken in by the first secretary of the Venezuelan embassy but was soon tracked down by government security forces, who broke into the diplomat's house and dragged Duarte away amidst kicks and blows from rifle butts. The Christian democratic leader was detained briefly, beaten, and interrogated, then dispatched to Guatemala. From there, he flew to exile in Venezuela. He left behind a country where aspirations for change had been dashed and where repression was once again the official antidote to dissent.