Sao Paulo players had to intervene and stop their own players after a knife was thrown onto the pitch.
The Brazilian side were taking on Palmeiras in an U20s clash at the Arena Barueri.
Supporters ran on to the pitch to confront the Palmeiras players before the ref held aloft a knife which had been thrown.
Sao Paulo were 1-0 down before the unsavoury scenes spilled onto the pitch during stoppage time at the end of the clash.
Fans jumped over barriers as they attempted to confront the Palmeiras players before the hosts prevented them from doing so.
One Sao Paulo ended up confronting his own fan before the pair grappled as the player attempted to pull him away.
Eventually the ref was seen picking up a small black knife with video footage showing it was thrown by a fan behind the goal, narrowly missing players as it landed in the penalty area.
DRADE (Police Station for Repression of the Crimes of Sports Intolerance) officer Cesar Saad said they need to find out immediately how the weapon was not confiscated.
He said: "In stoppage time, two fans invaded the pitch, one of them went up and physically attacked a Palmeiras athlete, and the second fan who practiced the invasion was contained by the São Paulo players themselves.
"At the same moment, some objects were thrown into the field.
"We tried to identify images from the press and fans, the stadium cameras and after a lot of analysis, listening to referees and athletes, we realised that along with the other objects, the knife was thrown on the lawn.
"Initially we thought that one of the fans would have invaded to try to attack a Palmeiras player with this knife.
"The referees themselves called me in the referees' locker room and showed an image that is circulating in WhatsApp groups and the press where it shows the knife along with other objects being thrown.
"It is obvious that it is up to the Civil Police to find out how this knife ended up inside the stadium, who did the search, how it was done, which gate the fan entered.
"Everything will be investigated by the police.
"It looks like the knife is inside a lunch box and when it is thrown, it opens and the knife jumps out.
"This was shown to the Palmeiras athletes, to the Palmeiras football director who saw the images at the police station and everyone could see that the fans who invaded the pitch, who are being punished by the Civil Police, were not in possession of this knife."