- Juan Martín Lucero (48')
- Lisandro Alzugaray (56')
Liga and Fortaleza drew 1-1 in regular time, carried the stalemate into extra time, but the Ecuadorians prevailed 4-3 in the penalty shootout to win South America's second most prestigious club tournament.
Juan Lucero gave the Brazilian club the lead in the 48th minute, but Liga de Quito's Lisandro Alzugaray got the equalizer six minutes later.
Fortaleza goalkeeper Joao Ricardo stopped the first penalty from veteran Peruvian striker Paolo Guerrero, but Liga's Dominguez then saved the shot taken by Silvio Romero.
Dominguez stopped Augusto to keep Liga in contention, then blocked Emanuel Britez to give the Ecuadorian team the title.
Liga also won the tournament in 2009 after beating Brazil's Fluminense in a two-leg final.
Fortaleza was the first team from Brazil's Northeast region to play in an international club final. Its fans were the majority in the 20,000-seat Domingo Burgueño Miguel Stadium in Maldonado.
The stadium in Uruguay lies more than 5,000 kilometers (3,100 miles) from the cities where Liga and Fortaleza are based.
"In the tough moments it was my family who lifted me up. This is a great new achievement for me, for my country, my club," Dominguez said. "Many people traveled for days by bus, by car. Now we will celebrate with them."
Argentina's Boca Juniors and Fluminense will play for the Copa Libertadores title next Saturday at the Maracana Stadium in Rio de Janeiro.
- Jesús Valenzuela