The former AC Milan forward intercepted a backpass and went over as he was challenged by Sao Paulo goalkeeper Rogerio Ceni.
Sao Paulo protested furiously, delaying the match for seven minutes before Pato finally converted from the spot.
"It was a disgrace, both players went for the ball and he went in with his foot raised and could have broken my foot," Sao Paulo captain Rogerio told reporters after Sunday's Paulista championship match at the Morumbi.
"It was 100 percent a penalty, if he hadn't stopped me, I would have scored into an empty goal," retorted Pato.
Jadson gave championship leaders Sao Paulo, already qualified for the quarter-finals, an early lead and Danilo levelled for Club World Cup winners Corinthians four minutes before half-time against the run of play.
Santos forward Neymar scored his first goal since February 10 to help his side to a 2-1 win over Oeste in another of Sunday's games.
Former Brazil full-back Branco quit as coach of Guarani after they lost 3-0 at home to Atletico Sorocaba, leaving them bottom of the table.
"The supporters don't deserve this," said the 1994 World Cup winner who played for Porto, Genoa and had a short spell at Middlesbrough in his club career.
The Paulista is one of a plethora of regional tournaments which kick off the Brazilian season.
