The official team bus had various missiles thrown in its direction by River Plate fans as it approached the El Monumental stadium in Buenos Aires, Argentina.
TV reports claimed the Boca players were vomiting in the dressing room.
There have also been unconfirmed rumours that the coach driver fainted.
Equally, there are suggestions that the pepper spray was used by police in an attempt to disperse the River Plate fans.
The incident occurred roughly 90 minutes before kick-off.
The first leg of the Copa Libertadores final, hosted by Boca Juniors, finished 2-2 two weeks ago.
Boca Juniors and River Plate are fierce rivals and the match itself is expected to be a feisty affair.
Further reports from Argentina claim that the Boca players are in no fit state to play the leg.