The goal came from a controversial corner awarded after a clearance by a defender, which was heading for the sideline, hit the linesman on the knee and went over the goalline.
Independiente lead the standings with 20 points from nine matches, two ahead of Godoy Cruz with Velez Sarsfield third on 15.
Independiente's win was soured by the loss of midfielder Walter Busse who broke both bones in his lower left leg early in the first half in a collision with Chacarita's Emanuel Centurion, he will have surgery on Monday.
Striker Federico Higuain was the toast of the wine-producing province of Mendoza after Godoy Cruz beat Atletico Tucuman 2-1 on Friday to go top temporarily.
In the week when the Real Madrid side of his brother Gonzalo were eliminated from the Champions League, Higuain scored both goals for Godoy Cruz including a stoppage-time winner to take his tally to five for the season.
South American champions Estudiantes ended a run of five games without victory in all competitions with a 2-0 win over Newell's Old Boys to boost their confidence for their Libertadores Cup Group Three commitments this month.
Title holders Banfield, fielding reserves to rest their first team for a Libertadores Cup Group Six match at home to Nacional of Uruguay on Tuesday, lost ground in a 0-0 draw with Arsenal.
Banfield are joint third with 2009 Clausura winners Velez Sarsfield, Estudiantes are fifth a point further back.
