Boca Juniors stayed top after winning 2-1 at third-placed Lanus and Banfield finally won after losing their opening six matches.
Troglio, who played for Argentina at the 1990 World Cup and becomes the third coaching change in seven rounds of the championships, had been in charge for a year and three months, an eternity in the topsy-turvy world of Argentine coaching.
"The best thing for everyone is for me to leave at this moment... and to clear the air," he told reporters after watching his winless team throw away a two-goal lead in Sunday's match.
Santiago Salcedo and Pablo Barzola scored from free-kicks to put Argentinos 2-0 ahead after 31 minutes but Gabriel Mercado, Guido Carillo and Mauro Fernandez scored in an eight-minute spell to give Estudiantes a 3-2 halftime lead.
Leandro Barrera equalised for Argentinos in the 84th minute, only for Mercado to snatch the winner two minutes later.
Argentinos have four points from seven games.
Banfield, where former Mexico coach Ricardo La Volpe took over two weeks ago, and Independiente have also changed coaches.
Banfield broke their duck with a 1-0 win at All Boys in La Volpe's second game in charge.
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