The victory ensured that city rivals Corinthians also qualified for the quarter-finals at Guarani’s expense.
An organised fan group for one of Brazil's biggest football clubs lambasted its own players for winning a game on Sunday, calling them "cowards" because the victory helped one of their biggest rivals qualify for the league playoffs.
Sao Paulo had already qualified for the last eight of the Sao Paulo state championship and they beat Guarani 3-1 even though they fielded a team comprising mostly of reserves.
The victory ensured that city rivals Corinthians also qualified for the quarter-finals at Guarani's expense.
That angered some fans, who wanted Sao Paulo to ease up so Corinthians would miss out.
"The important thing wasn't winning, it was smiling," the Independiente fan group, which has 95,000 followers, said on twitter.
"Board, coaches, players. Dishonor without limits," read another tweet. "When you need to win, you tremble. When it comes to being sneaky, you're filled with hypocritical modesty."
The group warned coach Fernando Diniz he must win the tournament – which Sao Paulo hasn't lifted since 2005 - or face the sack.
Organised fan groups wield unusual power in Brazil, where they can influence management decisions on choosing players and coaches.
The groups are among the most passionate and demanding supporters and have been known to harass players and invade training grounds when performances are poor.