Some 50,000 fans packed into the famous Bombonera ground to see the players train for Saturday's clash with their arch rivals and thousands more were locked outside.
Boca conceded it had been a misjudgement.
"There were more people than suitable," Boca president Daniel Angelici told the TyC Sports channel.
"Lots of people were left outside, we went too far and they have closed the stadium."
Angelici said the club aimed to contest the stadium closure on Friday, fearing that if Boca triumph in Saturday's match at River's Monumental stadium they would not be able to host a celebration there.
The two Buenos Aires teams drew the first leg 2-2 at the Bombonera on Nov. 11 and away fans will again be banned for deciding second leg of the final.
It is the first time Argentina's two biggest clubs have met in the final of the Libertadores, South America's equivalent of the Champions League.
(Reporting by Andrew Downie, editing by Nick Mulvenney)
