Wednesday's game was the second this week in the Copa Sudamericana competition to be suspended by crowd violence following ugly incidents in the previous night's match in Ecuador between Emelec and Olimpia.
Universidad de Chile were dominating the game at the Parque Central stadium and leading 2-0 when one of the linesman was hit in the 47th minute by what Uruguayan media identified as a roll of paper.
The official was knocked to the ground and received treatment for several minutes before the referee called the match off.
The South American Football Confederation (CSF) said on its website that it would meet later in the week to decide on the outcome.
The Chilean side won the first leg 1-0.
Tuesday's match at Emelec was called off in the 81st minute when fans hurled bottles onto the pitch, apparently in protest against their team's coach Juan Ramon Carrasco. Paraguayan side Olimpia were leading 2-1.
Former Uruguay coach Carrasco has had an unhappy two months in charge of the Guayaquil-based team.
