Fluminense, which had clinched its second title in three years two weeks ago, ended the tournament with a 2-1 loss to Vasco da Gama.
Third-place Gremio finished a point behind Atletico after drawing 0-0 with Internacional in the last match at Olimpico Stadium. The team will play at a new arena next year.
Last year's champion Corinthians, focused on the Club World Cup, lost 3-1 to fourth-place Sao Paulo.
Sport became the fourth team to be relegated, joining Figueirense, Atletico Goianiense and eight-time national champion Palmeiras.
Santos beat Palmeiras 3-1 on Saturday with a pair of goals by Neymar.
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