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.
Luis Checa got the ball rolling six minutes before the break and Ely Esterilla doubled the advantage seven minutes into the second half.
Christian Suarez helped himself to a brace in 12 second-half minutes to complete the comprehensive victory.
Also on Saturday, Deportivo Quito and Mushuc Runa were both 2-1 victors in home matches with Olmedo and Manta respectively, while on Sunday LDU Quito triumphed 1-0 at El Nacional.
'Obviously Messi is the best player in history and being compared to him means that you're doing things right, but I try to be myself': Barcelona star responds to comparisons with Argentine legend
'Darwin Nunez would be gold for Arsenal': Liverpool legend claims Gunners should have signed Uruguayan striker in January
