All Boys goalkeeper and captain Nicolas Cambiasso spilt a low cross from the right by Facundo Roncaglia into his net in the 18th minute to put Estudiantes in front.
Five minutes later, defender Cristian Vella also scored an own goal trying to divert another cross from the same wing by striker Rodrigo Lopez.
Striker Leandro Gonzalez completed the win when he headed home from close range at the far past following another cross from the right eight minutes into the second half.
A 0-0 stalemate at the Diego Armando Maradona stadium against struggling Quilmes left home side Argentinos Juniors as the only unbeaten team in the league.
Argentinos, who have two wins and five draws, could not find a way past bottom-placed side Quilmes, who have two points and are the only side without a win.
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