Boca Juniors captain Pablo Perez and midfielder Gonzalo Lamardo were treated at a hospital after River Plate fans threw projectiles at their team bus on its way to the River Plate stadium in Buenos Aires, Telam reported.
Some were also affected by tear gas and pepper spray used by police to quell the violence.
Carlos Tevez, Boca's veteran striker, told media that he and his teammates did not want to play, but were being forced to do so. They are forcing us to play the game.
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Second, physical injury was suffered by at least two Boca players as a effect of splinters of glass from the broken windows.
Boca's chairman requested the match be suspended, but South America's football confederation CONMEBOL initially would only delay kick-off for one hour, before extending that to two hours and 15 minutes.
A worrying aspect of South American football - especially viewed through the eyes of someone who lived through the bad, old days of the English game in the 1970s and '80s - is the occasional lack of basic measures in crowd control.
It is the first time ever it has been contested by two Argentine sides.
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"One can't play in these conditions", CONMEBOL President Alejandro Dominguez told reporters.
With a 2-2 draw carried over from the first leg, the second was due to be played at 8pm GMT on Saturday night. Fans of River Plate were seen attacking the bus of Boca as it neared the Estadio Monumental, and it turns out players of Boca were hurt as a result.
Television pictures showed Boca players emerge from the bus, which had several broken windows, clearing their throats and with eyes streaming from the effect of the gas.
"They were throwing pepper gas, stones, everything", Clarin website quoted Juan Carlos Crespi, a member of the Boca delegation, as saying. There were further scuffles as River fans, many of whom had been in the stadium for around six hours without seeing a ball kicked even in a warm-up, clashed with police on their way out of the stadium.
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Later, his ambulance was surrounded by River Plate fans as he left the hospital. No visiting fans are allowed in the stadium, following a 2013 ban on away fans to stop football related violence in Argentina.