Boca travelled across Buenos Aires with the final tied at 2-2 after the opening game at La Bombonera, but deciding a winner will have to wait.
As the visitor's bus made its way towards River Plate's stadium it was showered with projectiles, with some smashing windows of the vehicle.
Eventually the bus arrived at the ground, but reports suggested three players had to be taken to hospital for assessment, while some were believed to have been affected by the use of pepper spray.
Discussions led to several delays in the scheduled kick-off time and the match has now been suspended until 1700 local time (2000 GMT) on Sunday.
On a dramatic morning, CONMEBOL medical officials had earlier cleared Boca players to contest the second leg despite captain Carlos Tevez's insistence the squad is unable to play after the attack.
Alarming images showed Boca's bus windows being smashed by missiles thrown from assembled River Plate fans as it arrived at El Monumental.
Pablo Perez – who appeared to have cuts to his arm and eye – was taken to hospital for assessment, while reports suggest some of his team-mates were affected by the use of pepper spray.
Discussions resulted in an initial delay to kick-off that was subsequently extended to 1915 local time (2215 GMT). The rescheduled kick-off had initially passed without the match getting under way.
The new time came after CONMEBOL president Alejandro Dominguez released a statement signed by members of the governing body's medical department that described the injuries as "superficial".
It referenced "skin lesions in upper limbs, lower limbs, face and body" but said complaints of cornea damage "could not be verified".
"Given this situation, we consider that from a medical point of view there's no cause for the suspension of the match," the statement read.
Veteran striker Tevez contradicted that view, claiming shaken Boca players were being forced to take the field against their will.
"We cannot play. They are forcing us to play the match. I understand they [CONMEBOL] are under a lot of pressure," Tevez told Fox Sports Argentina.
"My headache is just now getting better. We have three team-mates that are in no condition to play.
"None of the River players came to ask how we were doing."