After dropping points in consecutive weeks - drawing with LDU Loja and losing to Deportivo Quito - Independiente returned to form away from home at the Stadio Olimpico Atahualpa in Ecuadorian Primer A action.
Fernando Guerrero's 52nd-minute strike was all that separated the two teams as hosts El Nacional slumped to their second defeat in three weeks.
Independiente are three points clear of Barcelona at the summit in the second phase of competition after 15 rounds.
Wednesday's only other match saw fourth-placed Emelec account for LDU Loja 3-1.
First-half goals from Fernando Gimenez and Marcos Mondaini, and Fernando Gaibor's strike eight minutes from time helped Emelec claim back-to-back wins.
Sergio Mina netted an injury-time consolation for LDU Loja, who are winless in four matches.
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