The defending champions have scored more goals than any other team this season but Gustavo Quinteros' men drew a blank for the second game running in a 1-0 setback on Saturday.
Miguel Bravo scored the only goal of the game at the Estadio Alejandro Serrano Aguilar as a superb defensive effort helped the underdogs, who were bottom at kick-off, to a third win on the bounce.
Despite the setback, defending champions Emelec sit five points clear at the summit with two matches remaining.
Second-placed Independiente del Valle had the chance to cut the gap to just three points, but they failed to take advantage after being held to a 0-0 draw at home to Universidad Catolica.
In the match between third and fourth, LDU Loja were on the receiving end of a 4-0 rout on their visit to the Estadio Monumental Isidro Romero Carbo to face Barcelona.
