Ruben Israel's Barcelona were narrow 1-0 winners at Universidad Catolica via Pedro Velasco's 16th-minute goal on Sunday.
Velasco rose highest from a corner and guided his header into the net, securing Barcelona's spot in the second stage of the Copa Libertadores.
Independiente del Valle's 4-0 rout of Manta on the same day was in vain as Barcelona topped the table by two points after 22 rounds.
However, the day belonged to Emelec after they done enough to top the aggregate standings, which takes into account the first phase.
Emelec - who finished third in the second phase - held a two-point lead heading into the final matchday and they maintained that advantage thanks to a 1-0 victory at home to bottom club Olmedo.
Miler Bolanos was the hero for Emelec, converting a 76th-minute penalty following a crude challenge inside the area.
The result capped a horrendous campaign for Olmedo (42 points), who were relegated from the top flight along with Manta (43 points) due to their standing in the aggregate table.
Emelec (88 points) finished two clear of Independiente and five above second-phase champions Barcelona.
In other results on Sunday, LDU Loja edged LDU Quito 1-0 thanks to Juan Villacres' goal three minutes from the end.
El Nacional accounted for Deportivo Cuenca 2-1, while Mushuc Runa and Deportivo Quito played out a goalless draw.
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