The knockout stage of the 2016 Campeonato Paulista began on 16 April with the quarter-final and was concluded on 8 May 2016 with the final.^[1] A total of eight teams competed in the knockout stage, with Santos being crowned champions after a 2–1 aggregate win against Audax.

All draws held at Federação Paulista de Futebol headquarters in São Paulo, Brazil.

With the exception of the final, which is played over two legs, each tie is played over a single leg, with the team with the best placing in the general table playing at home. The quarterfinals are played between the winners and runners-up of each group. In the semifinals the best team (first) will face the team with the worst campaign (fourth), while the second will face the team with the third best campaign.^[5]