Gremio travelled to Argentina and drew first blood in the opening leg of their quarter-final tie thanks to Alisson and Everton.
Independiente were awarded a 3-0 victory just hours before Tuesday's return fixture after Santos fielded an ineligible player.
Copa Libertadores holders Gremio suffered a narrow 2-1 loss away to 10-man Estudiantes in the round-of-16 first leg on Tuesday.
Barcelona's new Brazilian midfielder Arthur said it is a privilege to sign for the LaLiga giants.
Gremio had hoped to hold on to Arthur until the end of the year, but the midfielder has completed his long-awaited move to Barcelona.
Barcelona have successfully negotiated with Brazilian club Gremio to bring the transfer of midfielder Arthur forward from January.
Barcelona will not be bringing Brazilian midfielder Arthur to Camp Nou before the 2018-19 season, according to Gremio's president.
Gremio appear determined not to lose Arthur to Barcelona until their Brasileirao and Copa Libertadores campaigns end in December.
Gremio advanced to the knockout phase as Group 1 winners thanks to Wednesday's 1-0 victory over Uruguayan visitors Defensor Sporting.