Guido Carrillo scored a brace for Mauricio Pellegrino's men, with both goals assisted by fellow front-man Franco Jara.
Jara teed up the first goal of the game on 20 minutes at the Estadio Centenario Dr Jose Luis Meiszner, stabbing a through-ball for Carrillo, who pipped Quilmes goalkeeper Silvio Dulcich to roll the ball into the back of the net.
Quilmes' number nine Fernando Telechea then completed some fine lead-up work from the hosts, getting on the end of a dinked ball from Facundo Diz to lash home the equaliser, which went in off the left post.
Jonathan Silva regained the lead for Estudiantes in remarkable style, sending a 35-yard pearler into the back of the net via multiple deflections, the last of which was off goalkeeper Dulcich.
Jara was then the catalyst for Estudiantes' third, as he was pushed over in the box, got back to his feet, rounded the keeper and chipped a cross to Carrillo - who simply had to tap into the gaping net.
River Plate ensured Estudiantes would only hold a one-point buffer at the top, after winning 2-0 at home to Atletico Rafaela.
Colon, who entered the round level on points with Estudiantes, were held 0-0 at home to Boca Juniors.
Lanus made it back-to-back victories, as they surpassed San Lorenzo 4-1 on the road.
Jorge Valdez scored a brace for the winners, who sit fourth in the table, one point ahead of Gimnasia La Plata and San Lorenzo.
Gimnasia La Plata enjoyed a 2-0 home win over Arsenal, while Velez Sarsfield were humbled for the second match in succession, going down 2-1 away to Argentinos Juniors.
Rosario Central are unbeaten in three matches, after a scoreless stalemate at home to Belgrano.
Tigre made it two wins in a row, with a 2-0 home result over All Boys, while Racing Club were held by Olimpo 1-1 and Newell's Old Boys ended a four-match winless run in the league with a 1-0 triumph at Godoy Cruz.
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