Hardcore Boca fans on the terracing behind the goal River were defending in the second half lit flares and threw fireworks and objects into the penalty box causing referee German Delfino to halt play for nearly 10 minutes.
Delfino said he came very close to abandoning the match, that ended in a 1-1 draw between the bitter rivals.
This was the first "superclasico, the biggest match on the Argentine league calendar, at La Bombonera since River were promoted back to the first division after relegation in 2011.
"We have opened a case to see who's responsible. What we're investigating are fireworks being taken into the stadium," public prosecutor Martin Lopez Zavaleta told TN television on Monday.
"The (security) operation failed because there should not have been all those fireworks and banners inside the stadium. We confiscated film footage, we're not ruling anything out," he said.
"The investigation is to find out who failed and who didn't carry out their duties."
Delfino, quoted in the sports daily Ole, said: "We were close to suspending (the match)."
This would have likely resulted in Boca being docked points.
Boca fans lit fireworks and displayed banners mocking River for their relegation about 15 minutes from fulltime when rival coach Ramon Diaz was sent to the stands by Delfino for dissent.
As he walked off, Diaz made a gesture of denial with his index finger.
Diaz, who coached the team to a record seven titles in a previous period at River, returned to the club at the end of last year.