The former Espanyol striker, who spent 11 years in Spain before his problematic heart condition was diagnosed playing at high altitude in Mexico for Toluca in 2012, scored with a header in the 19th minute.
The Bolivian side, who had won last week's first leg 1-0 in Santa Cruz de la Sierra, had Argentine defender Mariano Brau sent off after an hour and conceded a second goal to midfielder Carlos de Pena in the 73rd when goalkeeper Carlos Arias let his shot slip from his grasp into the net.
Nacional go into Group Six with Newell's Old Boys of Argentina, semi-finalists last year, and former South American champions Gremio of Brazil and Colombia's Atletico Nacional.
Two players were sent off during Tuesday night's other match in Colombia where Independiente Santa Fe beat Mexico's Morelia 1-0 for an aggregate of 2-2 and a place in Group Four on the away goals rule.
Central defender Julian de la Cuesta scored the only goal at El Campin in Bogota in the 57th minute, three minutes after Morelia's Colombian midfielder Aldo Leao Ramirez had been shown a red card. Two minutes later the home side's Luis Seijas was also sent off.
Santa Fe, who reached the last four in 2013, face Brazilian holders Atletico Mineiro, Nacional of Paraguay and Venezuela´s Zamora in the group phase which starts next week.
(Writing by Rex Gowar in London; editing by Josh Reich)
