Luis Fernando Saritama put Deportivo ahead in the 29th minute with a free kick which flew past helpless Wilmer Zumba.
Jose Herrera headed Macara level in the 68th minute and former Ecuador midfielder Edwin Tenorio scored the winner with six minutes left.
Coach Carlos Sevilla had previously led Emelec to the title in 2001.
The squad included two survivors of Ecuador's 2002 World Cup squad, Tenorio and goalkeeper Geovanny Ibarra, and Leider Preciado who played for Colombia in 1998.
Hundreds of people invaded the pitch at the end of the game to celebrate. LDU were held 1-1 by army club El Nacional.
Meanwhile, in Peru, Deportivo San Martin won the second stage of the championship without kicking a ball when nearest challengers Sporting Cristal were held 1-1 by Alianza Atletico.
San Martin could win the overall title as well although, under the intricacies of the tournament's format, they may have to play a two-leg final against Universitario.
Carlos Lobaton gave Cristal an early lead but Marcio Valverde fired a 78th minute equaliser and their misfortune was complete when substitute Luis Hernandez was sent off after only 15 minutes on the field.
Universitario, who won the first stage of the championship earlier in the year, are due to face San Martin in the final but will lose the right to take part if they do not finish in the top seven of the second stage.
Universitario are 10th, two points outside the top seven, after a 2-1 win over Cesar Vallejo on Wednesday.
Alianza Lima, who sacked former Venezuela coach Ricardo Paez at the weekend, crashed to a 4-1 defeat at Cienciano in their first game under replacement Jose Soto.
Cienciano, themselves immersed in internal problems centred around coach Julio Cesar Uribe's insistence on fielding his son Edson in the team, took an early lead through Carlos Salom.
Mauricio Montes scored two more and Piero Alva added an injury-time penalty.
Alianza Lima are only two points clear of the relegation zone with two games left. Sport Boys, another traditional Lima club, have already been condemned to the drop.
