Cruzeiro, Libertadores favourites before they too were upset in the last-16, won the Mineiro, another of the many state championships that open the Brazilian season, when they beat arch-rivals Atletico 2-0 in the second leg of the final and 3-2 on aggregate.
Santos, the only Brazilian team to reach the Libertadores quarter-finals, retained the Paulista (Sao Paulo) title with a 2-1 home win over Corinthians at the Vila Belmiro following a goalless draw in last weekend's first leg.
Internacional were under pressure after a 2-1 home defeat by Penarol of Uruguay in the first knockout round of the Libertadores followed by a 3-2 loss at their Beira-Rio stadium by Gremio in the first leg of the Gaucho (Rio Grande do Sul) final.
They fell behind at Gremio's Olimpico on Sunday when left-back Lucio got behind the defence to open the scoring in the 16th minute.
Inter's fortunes changed when coach Falcao sent on substitute Ze Roberto after half an hour and in his first attack he crossed for young Brazil striker Leandro Damiao to equalise.
Ze Roberto also took the corner from which Andrezinho scored Inter's second goal and was the victim of the foul that led to the 73rd-minute penalty, converted by Argentine playmaker Andres D'Alessandro, that put them 3-1 up.
Striker Borges pulled a goal back 10 minutes from time for Gremio, putting the aggregate level at 5-5 and sending the final into a shootout.
Inter's goalkeeper Renan saved three penalties to secure the title for his team.
"Those on the bench, when they have a chance to go on, have to do something different," Ze Roberto told reporters.
"I got the chance in the first half and was able to contribute for us to win this title here in the Olimpico. Inter showed they are a champion team."
Three players were sent off in final minutes of the Mineiro (Minas Gerais state) decider at the Alligator's Arena in Sete Lagoas which is being used while the Mineirao stadium in Belo Horizonte is being refurbished for the 2014 World Cup finals.
The Brazilian championship, with the country's top 20 teams, kicks off next weekend.
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