It was the latest in a series of incidents involving ball boys in Argentina, who are often accused of time-wasting when the home team are defending a slender lead.
The ball boy, who Argentine media said played in River's youth divisions, dallied as he returned the ball for a goal kick in the 70th minute of Sunday evening's game.
After finally collecting the ball, a furious Pezzutti throw it back at the youth and was sent off. The ball boy was also ordered dismissed.
Relegation-threatened Gimnasia finished with nine men after Daniel Ramasco was also sent off for a second bookable offence in the 90th minute.
Colombian striker Radamel Falcao Garcia scored the only goal in the 59th minute of the Clausura championship game to give River a consolation win after their Libertadores Cup elimination last week.
The first ball boy row blew up at the start of the month during the derby between Gimnasia-La Plata and Estudiantes.
The referee added on six minutes of injury-time after the balls were hidden behind the substitutes benches in the second half with Gimnasia-La Plata leading 1-0.
But the tactic backfired when Estudiantes scored with the last kick of the game to draw -- and the hosts complained that too much time had been added on.
Velez Sarsfield stayed top of the Clausura table after coming back from 2-0 down to win 4-2 away to Colon.
Sebastian Prediger and Sebastian Sciorilli put Colon two goals ahead in half an hour and the hosts also hit the post just before the break.
The second half was a different story, which began when Jonathan Cristaldo scored from a rebound after Joaquin Larrivery's header hit the crossbar two minutes after the restart.
Hernan Lopez levelled from a penalty in the 67th minute, Juan Manuel Martinez then gave Velez the lead and Lopez added the fourth with five minutes left.
Velez lead the table with 25 points from 11 games, one ahead of Lanus who won 1-0 at Godoy Cruz. Defending champions Boca Juniors lost 2-0 at Rosario Central and dropped to 15th.
