The defending champions were held to a goalless draw mid-week and their recent stuttering form continued after they were beaten 2-0 at El Nacional on Sunday.
A scoreless opening period at the Estadio Olimpico Atahualpa was soon forgotten as Pablo Palacios broke the deadlock on the hour-mark.
Former Ecuador international striker Carlos Tenorio put the result beyond doubt 10 minutes later with his fourth goal in five games.
Emelec's lead at the summit is now one point, though they have played a game less than second-placed Independiente Del Valle, who edged lowly Mushuc Runa 1-0.
Elsewhere in Ecuador, LDU Loja consolidated third spot with a 1-0 victory over Manta thanks to Jonny Uchuari's first-half effort.
LDU Loja's triumph moves them within two points of top spot and just one adrift of second.
Barcelona extended their unbeaten streak to three games following a come-from-behind 2-1 win at home to Universidad Catolica.
Armando Wila put the visitors ahead after 21 minutes but second-half goals from Cristian Penilla and Flavio Caicedo secured all three points for Barcelona, who are level on points with Catolica in fifth position.
In other results, three goals in the opening half saw Deportivo Quito account for cellar dwellers Deportivo Cuenca 3-1, while LDU Quito and Olmedo played out a 2-2 draw.
