Starting from the quarter-finals, the teams played a
single-elimination tournament. The matches were played on a home-and-away
two-legged basis, with the higher-seeded team hosting the second leg. If tied on aggregate, the higher-seeded team would qualified.
Bracket Quarter-finals Group A Originally, the Group A would be played between the first stage winners
Chapecoense and the 8th place
Hercílio Luz. The match Hercílio Luz v Chapecoense, 0–0, was played on 25 April 2021 at
Estádio Aníbal Torres Costa in
Tubarão. The match Chapecoense v Hercílio Luz, 1–0, was played on 28 April 2021 at
Arena Condá in
Chapecó. Chapecoense won 1–0 on aggregate and qualified for the semi-finals. However, on 29 April 2021, the
FCF announced that was investigating Hercílio Luz to find out if they potentially fielded an ineligible player (
Alisson) against Brusque in the first stage. Due to this, FCF suspended the semi-finals between Marcílio Dias and Chapecoense. On 4 May 2021, Hercílio Luz were deducted three points and sanctioned with a fine of R$15,000 (reduced later to R$10,000) after they were punished by Tribunal de Justiça Desportiva do Futebol de Santa Catarina (TJD–SC). TJD–SC also annulled the results of the quarter-finals between Chapecoense and Hercílio Luz and ordered that the quarter-finals be replayed between Chapecoense and the new 8th place
Figueirense. ---- ----
Chapecoense qualified for the semi-finals. Group B ----
Brusque qualified for the semi-finals. Group C ----
Avaí qualified for the semi-finals. Group D ----
Marcílio Dias qualified for the semi-finals. Semi-finals Group F ----
Chapecoense qualified for the finals. Group G ----
Avaí qualified for the finals. ---- ;Notes
Finals Group H ---- ==General table==