Santos had three players sent off between the 24th and 82nd minutes at their Vila Belmiro stadium but held on to clinch the crown by virtue of their better record in the overall standings before the knockout phase.
"I think that with two (men) less the team were warriors and heroic. We more than deserve the title," said midfielder Ganso, who like two-goal forward Neymar is being touted by media and fans for a place in Brazil's World Cup squad.
Modest Santo Andre, who have never won the Paulista and are in the Brazilian championship's second division, failed to score a crucial fourth goal despite an advantage of one man from the 37th minute and two in the final eight.
Striker Nunes rattled Santos by putting Santo Andre ahead in the opening minute but Neymar equalised five minutes later from captain Robinho's pass.
Santo Andre had reached the final at the expense of big teams Corinthians, Palmeiras and Sao Paulo, and went ahead again in the 20th minute when Ale headed home a corner but 18-year-old Neymar again pulled Santos level.
RED CARDS
The teams were reduced to 10 men each when former Brazil fullback Leo and Nunes fought and were both shown the red card with 24 minutes on the clock.
Marquinhos of Santos was also shown a straight red in the 37th minute for a tackle from behind on fellow midfielder Branquinho.
Santo Andre soon took advantage with Branquinho netting their third goal two minutes before the interval but they were unable to score again despite constant pressure throughout the second half.
Substitute midfielder Roberto Brum left Santos with eight men when he was dismissed for a foul on Romulo but the closest Santo Andre came to a winner was when Rodriguinho hit the bar in the last minute.
"I'm exhausted... it wasn't easy keeping the ball up in attack near the end," the 20-year-old Ganso told reporters.
Gremio clinched the Gaucho championship in the southern state of Rio Grande do Sul and Atletico Minerio lifted the title in the state of Minas Gerais.
The Brazilian championship starts next weekend but will take a break during the World Cup.
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