Gustavo Quinteros' men wrapped up a 3-0 second-leg victory at home to Barcelona, who played 80 minutes with 10 men.
Alex Bolanos was sent off for a crude challenge on brother Miler Bolanos, who is on loan at Emelec from LDU Quito.
That made the equation tough on Ruben Israel's side, and compounding their numerical disadvantage was a well-created opening goal for the hosts 12 minutes later.
Angel Mena was the goal-scorer but a fine ball through the middle of Barcelona's defence from Bolanos got in behind the back four and drew the goalkeeper - and Mena was on hand to power a shot high into the net to put one hand on the trophy for Emelec.
Bolanos sealed the silverware late for Emelec with a double, striking in the 81st and 87th minutes to deny Barcelona the chance to win two titles in three years.
A Bolanos header from a cross in from the left sparked wild celebrations at the Estadio Banco del Pacífico in Guayaquil, before Mena was through on goal again only to square a pass for Bolanos to finish his brace.
