Henry Canga's 85th-minute goal was enough for Jorge Celico's men, who are two points clear of Emelec.
Canga rose highest to head in a set-piece late on, condemning fourth-placed El Nacional to their second straight loss.
Emelec were held to a 0-0 draw at home to LDU Quito to see them slip behind the league leaders.
Independiente struck three times in the first half on their way to a comfortable 3-0 victory at home to Barcelona.
Junior Sornoza netted a brace in the opening 16 minutes before Daniel Angulo gave the hosts their three-goal advantage just after the half-hour mark.
Deportivo Quito ended a run of three straight losses in the league thanks to Federico Nieto, whose 88th-minute goal saw them past Manta 1-0.
In a round of several late goals, Adrian Moran rescued a point for Macara as they drew 1-1 at home to Deportivo Cuenca thanks to his 90th-minute effort.
The clash between struggling sides LDU Loja and Deportivo Quevedo was postponed.
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