The referee then debated the decision with his assistants but several minutes more elapsed before he restarted play with a corner to Palmeiras.
Players from both teams surrounded the officials and riot police appeared on the touchline to prevent the same sort of scuffles that marred the first leg, when two players were sent off.
Palmeiras won that game 1-0 but Corinthians evened things up away from home in the second minute when Rodriguinho side-footed home after a nice cut back from Mateus Vital.
In the shoot-out, Cassio saved penalties from Dudu and Lucas Lima and Corinthians scored four of their five to triumph 4-3.
In Rio de Janeiro, penalties were also needed for Botafogo to overcome Vasco da Gama and lift the Carioca championship.
Carli scored in injury time to give Botafogo a 1-0 win and even the scores after Vasco's 3-2 win in the first leg.
In a repeat of what happened in Sao Paulo, Botafogo's Paraguayan goalkeeper Gatito saved twice as Botafogo won 4-3 on penalties.
In Minas Gerais, Cruzeiro won the Minas state championship by beating city rivals Atletico Mineiro 2-0 to take the title on away goals after losing 3-1 away in the first leg.
Thiago Neves and Giorgian De Arrascaeta scored for Cruzeiro, with Atletico having two men sent off.
Gremio beat Brasil de Pelotas 3-0 away from home to secure their first Rio Grande do Sul state championship in eight years. The Copa Libertadores champions won the first leg 4-0 at home last week.
(Reporting by Andrew Downie; Editing by Ian Chadband)
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