The Brazilian had been booked just before half-time and was shown the red card after the final whistle when he kicked the ball at an opponent.
Players from both teams then became involved in a melee, with Neymar appearing to headbutt an opponent, and referee Enrique Osses also produced a red card to Colombia’s Carlos Bacca.
And if Neymar was sent off for violent conduct, then the Barcelona forward will miss his country’s quarter-final tie – should they progress that far in the tournament – although he will definitely be out of their final group game against Venezuela on Sunday.
The scrappy game threw up few clear chances but Colombia were stronger than their more illustrious rivals, and recorded only their second win in 10 Copa America encounters against Brazil.
Defender Jeison Murillo seized on a loose ball to get the all-important goal nine minutes before the break after a Juan Cuadrado free kick had bobbled around in the box.
Roberto Firmino should have equalised for Brazil just before the hour mark but he skied a golden chance over the bar with the goal gaping.
The win leaves Colombia and Brazil tied at the top of the group along with Venezuela, who play Peru on Thursday.
Brazil could have secured a spot in the quarterfinals with a win over Colombia, but now it will decide its future against Venezuela on Sunday.
“Colombia showed that it is a very experienced team,” Brazil coach Dunga said.
“Our players at times got caught in their provocations and forgot to play football. Brazil has to play football. Brazil can’t go to war, we have to focus on what we do best, which is play football.”