Neymar's brace helped Santos beat Guarani 4-2 and become the first team in 43 years to win three straight Sao Paulo state championships.
Santos equalled their own record from 1967-69, when Pele was still playing, as they lifted the Sao Paulo title after winning 7-2 on aggregate following a 3-0 victory in the first leg last week.
Neymar, 20, played a role in the first as he passed to Elano, who fed Alan Kardec to open the scoring in the first two minutes. But three minutes later, goalkeeper Rafael spilled a cross and Fabinho equalised.
Neymar's penalty put Santos ahead once more, but Bruno Mendes got Guarani back into the game again in the 17th minute.
After a blistering opening, Santos had to wait until the 73rd minute to take control as Neymar - who has scored 27 times in 24 matches this year - smashed home a shot and Kardec rounded off the win in the final minute.
"It's been a great year for me and for Santos," Neymar said after the game. "I never expected this would be happening."
In the Rio de Janeiro state tournament, Fluminense beat Botafogo 1-0 to win their first title since 2005 after a 4-1 first leg victory last week.
Internacional came from behind to beat Caxias do Sul 2-1 to win their 41st title in the Rio Grande do Sul state championship, while Atletico Mineiro beat America 3-0 to win the Minas Gerais state title unbeaten.