Rodríguez had been Alfredo Stroessner's closest confidant for 35 years. The two became so close that Rodríguez' daughter married Stroessner's elder son. However, relations between the two grew increasingly strained in the late 1980s. As the decade wore on, Rodríguez cultivated ties with the "traditionalists" in the long-dominant Colorado Party. This element of the party had supported Stroessner throughout his three-decade rule, but had come to favor a more humane way of governing. Matters came to a head in January 1989, when Stroessner relieved several generals of their commands and replaced them with men thought to be unquestionably loyal to him. Later that month, Stroessner closed all of the country's currency exchanges. This appeared to be a direct strike at Rodríguez, who ran one of the largest exchange houses in the nation. On February 2, Stroessner summoned his former ally and gave him an ultimatum—either accept appointment in the less important position of defense minister or retire. It was reported that Rodríguez avoided the reunion by faking a leg injury, going as far as having a fake cast put on one of his legs. Rodríguez gave his answer on the night of February 3 when he launched a violent coup. Rebel troops and tanks surrounded the headquarters of the Presidential Guard in Asunción. The coup had the backing of much of the Roman Catholic Church and of the United States, who no longer required Stroessner as an ally in the Cold War. With this support, the coup quickly succeeded, with Stroessner resigning only hours after hostilities began. However, some 500 soldiers on both sides are believed to have died as a consequence of Stroessner's capture. He was released and fled into exile a few days later, eventually taking refuge in Brazil. A couple of weeks following the coup, former interior minister Edgar Ynsfran, a former Stroessner ally who now sided with Rodríguez, told reporters that Rodríguez had begun planning the coup toward the end of December 1988.
Presidency
Upon taking office, Rodríguez canceled most of Stroessner's most repressive measures. He abolished the death penalty and tried to imprison some leading members of the Stroessner government. He also formally canceled the state of siege that had been in place for virtually all of Stroessner's rule; while it had nominally been repealed in 1987, its substance had remained in place in the form of draconian security laws. Over the course of the following week, the military was purged of Stroessner's loyalists, and the commanders of the six rebellious army divisions were promoted to replace them. As provisional president, Rodríguez dissolved Congress on February 9 under a provision in the 1967 constitution that allowed the president to dissolve the legislature if he felt it had acted in a manner that distorted the constitutional separation of powers. He issued a decree setting new elections in May, and announced that all non-Communist parties would be allowed to compete. This was a remarkable turn in a country where the opposition had been barely tolerated for much of its history, particularly during Stroessner's rule. Indeed, at the time of the coup, the country had only known two years of pluralism in its entire history. A presidential election for the balance of Stroessner's term was also held in May, since the constitution required new elections to fill out the term of a president who resigned less than two years into his term. Rodríguez ran as the Colorado candidate and was elected with 76 percent of the vote in what was the closest thing the country had seen to a free and fair election up to that time. Soon after the ouster of Stroessner, the Rodríguez government was contacted by representatives of the People's Republic of China, inviting Paraguay to end its long-standing diplomatic relations with the Republic of China and to recognize PRC instead. However, Rodríguez accepted the arguments of the Taiwanese ambassador Wang Sheng that continuing the relationship with ROC, and thus keeping Taiwan's development assistance and access to Taiwan's markets, would be more advantageous for Paraguay.
End of rule and death
In 1992, Paraguay adopted a new constitution. It limited the president to a single five-year term. The term limit retroactively applied to Rodríguez, even though he had promised that he would not run for a full term in 1993. Fears of a coup were only allayed when he signed the new constitution into law on June 22. He stepped down as president on August 15, 1993—the first Paraguayan president in decades to leave office at the end of his term. He was succeeded by Juan Carlos Wasmosy, who like Rodríguez was a member of the Colorado Party. Rodríguez died in New York City in 1997 after a long battle with cancer.