Angel Mena opened the scoring for Gustavo Quinteros' side after only 11 minutes before Enner Valencia doubled the lead just before half-time.
The victory means Emelec are deadlocked on top of the standings with Universidad Catolica, who are also on 21 points and overcame Macara 1-0 on the road.
Federico Laurito scored the only goal of the game in the 45th minute.
Deportivo Quito is in third position, four points off the leaders, after a 0-0 draw at home against rivals LDU Quito.
LDU Loja won their first game in seven after a 3-1 triumph over Barcelona.
The only goal of the first half came through Erick Castillo's 36th-minute opener before Armando Wila made the advantage two goals on 50 minutes.
Barcelona kept themselves in the game with a 76th-minute goal from Wilder Medina but seconds later, their own defender, Jose Perlaza, secured victory for Loja with an unfortunate own goal.
In other results, Manta and Deportivo Quevado traded a goal in each half while Independiente fought out a goalless draw against El Nacional.
