|Miranda shows off the trophy [EPA]
Sao Paulo won the Brazilian championship for the third year running and a record sixth time overall when they beat Goias 1-0 away in their final match.
Striker Borges scored a controversial winner in the first half for Sao Paulo, who had needed only a draw to wrap up the title on Sunday.
At the other end of the table, Figueirense and former South American champions Vasco da Gama were relegated, joining Ipatinga and Portuguesa in Serie B next season.
The tournament ended under a cloud after the Brazilian Football Confederation (CBF) changed the referee for the Sao Paulo game on Saturday.
The CBF replaced Wagner Tardelli with Jailson Macedo Freitas as a precautionary measure after saying they had been told of a plot to manipulate the result.
They emphasised Tardelli's honesty in 20 years as a referee but did not give any more details.
Sao Paulo, who have won their last three titles under coach Muricy Ramalho, finished the 38-match campaign with 75 points, three ahead of second-placed Gremio.
Ramalho's team staged an impressive rally in the second half of the tournament, having been fifth and 11 points behind Gremio just past the halfway mark.
The only goal came in the 22nd minute when Sao Paulo goalkeeper Rogerio Ceni's free kick was parried by Harlei, Hugo picked up the rebound and fed Borges who scored from close range amid Goias protests he was offside.
Soares in vain
Gremio beat Atletico Mineiro 2-0 with a Tcheco penalty and Soares header but their win was in vain.
|Vasco's glory days with Romario are well behind them [GALLO/GETTY]
Cruzeiro and Palmeiras finished third and fourth to follow Sao Paulo and Gremio into next year's South American Libertadores Cup.
Cruzeiro thumped Portuguesa 4-1 while Vanderlei Luxemburgo's Palmeiras clung on to fourth spot despite losing 1-0 at home to Botafogo.
At the other end, Vasco ended a season in which they got through five coaches by losing 2-0 at home to Vitoria and dropping into the second division for the first time.
Vitoria, whose bus was pelted with bottles and stones as it pulled into the Sao Januario stadium, went ahead when Leandro Domingues finished off a neat move in the 22nd minute.
Ricardinho added a breakaway goal in the 75th to seal Vasco's fate as they finished 18th in the 20-team table with 40 points.
The defeat completed a bitter season for Vasco coach Renato Portaluppi, who earlier this year was in charge of Fluminense when they lost the final of the Libertadores to Ecuador's LDU.
Figueirense beat Internacional 3-1 but finished 17th, below Nautico on goal difference, and were relegated after six seasons in the top flight.
Kerrison (Coritiba), Washington (Fluminense) and Kleber Pereira (Santos) finished as joint top scorers with 21 goals.