Nacional have been fined $80,000 (£57,500) and their fans banned for three games after some taunted Chapecoense about the plane crash which killed 19 players and staff.
During a Copa Libertadores match in January, some fans of the Uruguayan club made gestures referring to the 2016 crash involving the Brazilian side.
Nacional said the “horrendous” incident brought a “deep sense of shame”.
Conmebol, South American football’s governing body, banned Nacional fans for their next three continental away games.
“Unfortunately, many sick minds channel their irrationality to sporting scenarios”, Nacional said in a statement shortly after the incident on 31 January.
The taunts were made during Nacional’s 1-0 first-leg win at Chapecoense in the second stage of Copa Libertadores qualifying.
They won the second leg 1-0 at home on 7 Feb to complete a 2-0 aggregate victory.