Santos lost their first game of the year when they conceded two late goals and went down 2-0 at home to humble Sao Bento in the Paulista championship on Saturday.
Sao Bento, coached by former Colombia midfielder Freddy Rincon, went ahead with three minutes left with a Roberto Santos header as they picked up their second win in nine outings.
Sergio Junior added the second in injury time with a long-range shot that caught goalkeeper Fabio Costa off guard.
Santos, who had won nine and drawn one of their previous games this year, including two in the Libertadores Cup, stayed top of the Paulista (Sao Paulo state), the largest of the regional tournaments that kick off the Brazilian season.
Vanderlei Luxemburgo's team have 22 points from nine games.
Brazilian champions Sao Paulo moved into second place, one point behind, after a 4-2 win at America-Sao Jose do Rio Preto.
Souza, Hugo, Josue and Leandro shared the goals as Sao Paulo raced 4-0 ahead in just over an hour. Rafinho and Adriano Peixe pulled two back for the hosts.
Corinthians and Palmeiras, the other two of the big four alongside Santos and Sao Paulo, both failed to win.
Gilsinho scored twice, the second in the fifth minute of injury-time, as Paulista sank Corinthians 3-2 despite having Marcus Vinicius sent off after only three minutes.
Corinthians later had midfielder Roger dismissed along with coach Emerson Leao.
Palmeiras were held 1-1 at home by underdogs Rio Claro.
Vasco and Fluminense shared eight goals in a dramatic match in the Carioca (Rio de Janeiro state) championship.
Leandro Amaral scored a hat-trick for Vasco as they came from 4-2 down to snatch a point. Diego notched the other while Soares scored twice for 'Flu' and Cicero and Alex Dias once each.
Vasco da Gama, America-Rio de Janeiro, Madureira and Flamengo qualified for the semi-finals of the championship's first stage.
Flamengo, playing only three days after facing Bolivia's Real Potosi at nearly 4,000 metres above sea level in the Libertadores Cup, went through despite crashing 4-1 to Madureira.
After facing driving rain and near freezing temperatures in the Andes on Wednesday, Flamengo this time had to contend with a burning tropical sun and temperatures of over 30 Celsius in their afternoon match.
