Chapecoense are docked three points for fielding a suspended player and opponents Lanus awarded a 3-0 win.
Chapecoense won the Santa Catarina state championship on Sunday to lift their first title since most of their team died in a plane crash last November.
Chapecoense beat Atletico Nacional 2-1 in the first leg of their South American Supercup final on Tuesday as the game was marked by memorials to those killed in an air crash before the teams' scheduled Copa Sudamericana final last November.
Colombia's Atletico Nacional arrived in southern Brazil to fanfare on Monday for the first leg of the South American Supercup final against Chapecoense, a team that was almost wiped out in a plane crash before their scheduled meeting last November.
Chapecoense have named Neto and Alan Ruschel, two of the survivors of the tragic plane crash which decimated the club, in their Copa Libertadores squad.
Brazil beat Colombia 1-0 in a benefit match for the families of those killed in the Chapecoense air disaster but Wednesday's game in Rio de Janeiro was marred by a disappointing turnout.
Atletico Nacional collected the Fair Play prize at Monday's FIFA awards ceremony after the Colombian side requested Chapecoense receive the Copa Sudamericana title following a plane crash that decimated the Brazilian club.
The pilot in the plane crash that killed 71 people traveling to Colombia on a Bolivian charter including footballers from Brazil had not flown enough hours to pilot commercial flights, a copilot's attorney said Saturday.
Bolivian authorities detained on Tuesday the chief executive of airline LaMia, the owner of the plane that crashed last week in Colombia and killed nearly all of Brazil's Chapacoense soccer team, prosecutors said.
Brazil have invited Colombia to play a friendly match next month with proceeds from the game going to families of the Chapecoense players and staff killed in the Medellin air crash, a Brazilian Football Confederation (CBF) spokesman told Reuters on Monday.
Chapecoense's opponents in the last game of the Brazilian league season said they would not play the match out of respect for the stricken club who lost most of their players in a plane crash.