After his impressive displays for Argentinos Juniors in the 1985 Copa Libertadores, the Argentine coach Carlos Bilardo called Batista up for a friendly against Mexico on 14 November 1985 in a game that ended in a 1-1 draw. With the 1986 FIFA World Cup soon looming, Batista quickly went on to establish himself as a first choice player within the Argentina national football team. Despite his limited international experience, he played in every game throughout the tournament, which Argentina eventually won. An established regular within the squad, Batista played in the 1987 Copa América, 1989 Copa América and 1990 FIFA World Cup, which Argentina came runner-up in.
After the 2010 World Cup, Argentine national team manager Diego Maradona did not renew his contract, and Batista was appointed as caretaker manager on 27 July 2010. In his role, Batista led Argentina to two wins (1–0 over Ireland and 4–1 over World Cup holders Spain) and suffered a defeat against Japan 0–1. Three months later, he was named the official head coach of the Argentine national team. In his first match after being officialized as Argentina's coach, his team defeated Brazil 1–0, with a 90th minute goal by Lionel Messi. On 25 July 2011, the AFA announced that Bastita had stepped down as manager of the Argentine national team after poor results in Copa America.