The sanction on Ronaldinho's Brazilian club was imposed "for lighting of flares (by fans), a lack of proper security guarantees and non-authorised people entering the field of play," the regional governing body CONMEBOL said on its website (www.conmebol.com) on Tuesday.
The Paraguay-based organisation added that Atletico, who beat Olimpia of Paraguay on penalties after an aggregate 2-2 draw over two legs to win the South American club crown for the first time, had the right to appeal.
Corinthians, Atletico's predecessors as Libertadores Cup champions, were handed a lengthy ban on their supporters after a Bolivian boy was killed by a firework allegedly launched by some of their fans at a match away to San Jose in February.
Twelve Corinthians fans were arrested on orders from a prosecutor in Oruro.
Corinthians were also fined $200,000 but the ban on their fans at home matches in Sao Paulo was lifted in March after they had played one more match in the South American club championship.
Flares are a common sight at matches in South America where supporters sneak them into stadiums past lax security controls.