Argentina president Mauricio Macri last week declared he wanted visiting supporters to be able to attend the Superclasico, with only home fans having been present for matches between the two arch-rivals in Buenos Aires since 2014.
The city's security minister Martin Ocampo subsequently stated 4,000 opposition spectators would be present at each leg.
However, Boca and River have reached an agreement contrary to that to avoid restricting the seats available to its followers.
"Boca Juniors and River Plate have reached an agreement for the Copa Libertadores final to be played without the presence of away fans," read a statement released by Boca.
"This was agreed [on Monday] afternoon, following a meeting of the presidents of both clubs, Daniel Angelici and Rodolfo D'Onofrio, in the Argentine Football Association headquarters with its president Claudio Tapia present.
"At the meeting, the presidents of both clubs agreed that despite the local and international appeal generated by the Superclasico with the presence of both sets of fans, this could create problems for members of both clubs.
"In addition to the 4,000 seats for the away fans, thousands of other seats would also have had to be restricted in order to place an empty space in between as a safety area, narrowing down considerably the available space for the home fans.
"Despite this decision, Boca Juniors and River Plate value and recognise the interest of president Mauricio Macri in promoting the presence of away fans in the two legs of the final that will have historical significance.
"To that effect, both clubs commit to take all the necessary measures to make it possible for the presence of both fans in each league match."
The first leg will take place at La Bombonera on Saturday, with the return fixture at El Monumental scheduled for November 24.