South American champions Estudiantes have 16 points from six matches. They are two points in front of Banfield, who beat Newell's Old Boys 2-1 on Friday, and three ahead of Rosario Central.
Striker Jose Luis Calderon, 38, put Estudiantes ahead in the 12th minute when he turned in a left cross at the far post for his 299th career goal.
Two minutes after the break, striker Martin Palermo volleyed an equaliser after a poor clearance out of defence.
Boca had little time to enjoy the goal, though. Less than three minutes elapsed before winger Enzo Perez rifled in the winning goal unmarked on the right after the Boca defence failed to intercept a low cross from the left.
Boca have five points, having started the season as favourites under returned coach Alfio Basile, who led them to two league titles in his previous spell at the club.
Rosario Central lost their unbeaten record when they were beaten 1-0 at home by Colon striker Fernando Nieto's goal.
Promoted Characita Juniors marked the debut of their new coach Fernando Gamboa, by ending their run of five defeats with a first victory, 1-0 against Arsenal, to climb off the bottom.
Striker Gabriel Hauche, included in Diego Maradona's Argentina squad of home-based players for next week's friendly against Ghana, hit a hat-trick in Argentinos Juniors' 4-2 win away to Godoy Cruz on Friday.
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