The game began with two quick-fire goals as the midfielder put Boca ahead after four minutes with a low shot which crept inside the near post, before Matias Mirabaje volleyed an equaliser three minutes later.
Paredes put Boca back in front before half-time when he finished a sweeping move from midfield, firing in another low shot from outside the area.
Boca's third goal was scored by 39-year-old defender Rolando Schiavi, who snapped up a rebound midway through the second half as San Lorenzo completed their seventh game without a win.
Boca coach Julio Falcioni, suspended after being sent off in last week's Superclasico against River Plate, watched from the executive boxes and maintained his media silence in protest at criticism of his side's performances.
Boca are fourth in the table with 22 points from 13 games and San Lorenzo are 18th with 12.
In the relegation standings, which are decided over a three-year period, San Lorenzo are 19th out of 20.
Facundo Ferreyra scored a hat-trick to lead Velez Sarsfield to a 5-1 win at Arsenal in another of Saturday's games.
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