The league match at Audax's Bicentenario ground in La Florida on Sunday was called off in the 58th minute when visiting fans threw stones and launched fireworks and flares onto the pitch.
Audax were leading 3-1 when international referee Enrique Osses took the players off the pitch and were declared winners by Chilean governing body ANFP.
"It was decided to declare the match finished. This is the result of a vote by the board," ANFP executive secretary Oscar Fuentes said, adding the voting was 4-1 in favour.
Fuentes said those who voted against playing the remaining 32 minutes did so "because basically to do so would be a bad sign, that a delinquent can have some influence on the progress of a match".
Although the ANFP did not announce sanctions, Fuentes said it would opened court proceedings against anyone found responsible for throwing stones onto the pitch.
Colo Colo, one of Chile's leading clubs and the only one to have won the Copa Libertadores, are struggling in 12th place with 11 points from nine matches, 11 behind leaders Union Espanola, in the Chilean Apertura championship.
Audax, whose forward Sebastian Saez scored a first-half hat-trick against Colo Colo, are 14th with nine points after their second win.