The result means that Independiente, who earlier in the day were awarded a 3-0 first-leg win after Santos were adjudged to have used an ineligible player, qualified for the quarter-finals of South America's premier club competition.
Tuesday's game at the Pacaembu stadium was drifting towards a stalemate when Santos fans began throwing missiles towards the Independiente bench and onto the pitch with some eight minutes remaining.
Scores of fans then stormed the perimeter fence, prompting police to beat them back with batons.
A few managed to scale the barriers and get onto the pitch as police and supporters clashed at the bottom of the terraces. Police then launched percussion grenades to quell the violence.
The Chilean referee halted the game and a few minutes later took the teams to the dressing rooms and abandoned the match.
The trouble came at the end of a tumultuous day for the South American Football Confederation CONMEBOL.
Just hours before kick off it ruled that Brazilians Santos had fielded an ineligible player in the 0-0 first-leg draw in Argentina last Tuesday and therefore awarded Independiente a 3-0 win.
CONMEBOL said the player, Uruguay international Carlos Sanchez, had not served the entirety of a ban handed out in 2015 when he played for River Plate.
Santos said they fielded Sanchez after CONMEBOL's own online system showed the player had no outstanding bans.
Santos appealed the sanction and Sanchez was cleared to play in Tuesday's return leg but the decision to give Independiente a 3-0 win from the first match stood, infuriating the club and their fans, who had bought all 45,000 tickets for the game.
Tuesday's trouble brought back memories of the Copa Libertadores game between Brazil's Corinthians and River Plate at the Pacaembu stadium in 2016.
Corinthians fans invaded the field and were beaten back by police after they were knocked out the tournament by the Argentine side.
The referee abandoned the match with five minutes remaining and River 3-1 up.
(Reporting by Andrew Downie; Editing by Toby Davis/Peter Rutherford)
