Christian Cordero converted an 82nd-minute penalty to help third-bottom Mushuc Runa to victory at the Estadio del Mushuc Runa Sporting Club.
The result extended Mushuc Runa's winning run to four games and saw the club finish on 26 points from 22 matches, three points clear of cellar-dwellers Deportivo Cuenca, who came from behind to beat Universidad Catolica 2-1.
Sunday's loss mattered little to Emelec after they were officially crowned champions last week.
Emelec topped the standings with 44 points, four ahead of Independiente del Valle after their rivals played out a 1-1 draw at Deportivo Quito on the final day.
Jose Cortez gave the home side a surprise lead in the 22nd minute, rising highest to head the ball into the net.
Just as Deportivo Quito seemed on track for their second win in six games, Independiente were awarded a penalty with eight minutes remaining.
And Junior Sornoza made no mistake from the spot, sending the goalkeeper the wrong way.
In other results, Alejandro Villalva bagged a brace as El Nacional upstaged third-placed LDU Loja 2-0.
Villalva opened the scoring in the 28th minute and put the result beyond doubt in the closing stages.
LDU Loja ended the season a point clear of Barcelona, who could only manage a goalless draw at home to Olmedo.
Meanwhile, second-bottom Manta snapped a two-game losing streak with a 2-0 triumph at LDU Quito.
