Ecuadorian Primera A Review: Barcelona win El Clasico del Astillero
Ruben Israel's men, on return from the international break, required a 75th-minute goal from Ismael Blanco to extend their league winning streak to four matches.
Israel, however, was less than impressed with their method of victory, claiming his side were "uncomfortable" in the first half.
The win came at a cost too, with Matias Oyola (thigh) and Mario Martinez (knee) ruled out of their Copa Libertadores trip to Paraguay to take on Libertad on Wednesday.
Barcelona are two points clear in first spot, after Mushuc Runa slipped up again.
At home to Independiente del Valle, Mushuc Runa needed a 90th-minute equaliser from Maximiliano Barreiro to salvage a 1-1 draw and avoid consecutive defeats.
Independiente remain unbeaten with two wins and two draws, and have two games in hand on the leading teams.
LDU Loja celebrated their first win in four, downing cellar-dwellers Manta 2-0.
Jonny Uchuari and Danilo Carando were the goal scorers for Loja, who sit third on nine points - four behind Barcelona, and goal difference ahead of Deportivo Cuenca (fifth) and El Nacional (sixth).
Cuenca equalised late away at LDU Quito in a 1-1 stalemate, Alejandro Frezzotti netting in the 88th minute for the visitors.
El Nacional took the points away at winless Universidad Catolica 2-0, Pablo Palacios and Jorge Valencia on target in the first half.
Deportivo Quito broke through for their first win of the season, downing fellow strugglers Olmedo 2-0.