The Argentine side must also play its next 14 matches in Conmebol tournaments without its fans - seven at home and seven away - and pay a $250,000 (£186,000) fine, among tough sanctions, according to the ruling seen by AFP.
Nineteen people were hurt after fans hurled knives, sticks and stun grenades during the last-16 second-leg encounter on August 20 at Libertadores de America stadium in Buenos Aires.
The match was 1-1 when it was suspended in the 48th minute, before being called off.
Universidad de Chile now advance to the Copa Sudamericana quarter-finals, where they will face Alianza Lima of Peru.
But the Chilean club also faces sanctions.
It was fined $270,000 (£200,000) and barred from having fans at its next 14 international matches.
The tough ruling, seen as sending a strong message on stadium violence, can be appealed.
Conmebol threatened both teams with even harsher punishment in the event of repeat unrest.
The organisation also ordered the two teams to conduct campaigns on social media and in their stadiums against "racism, discrimination, and violence."
The violence flared at half-time when fans of the Chilean side began throwing stones, sticks, bottles, and seats at home supporters.
Independiente fans then rushed the visitors' enclosure - stripping, beating, and bloodying Chilean fans in some of the worst sporting violence South America has seen in years.
One Chilean fan threw himself from the top of the stands to escape attack.
Chilean President Gabriel Boric at the time accused the Independiente fans of "lynching" their rivals.
