At least 33 suspected assailants were killed early on Tuesday during a new round of attacks on police.
Authorities found 18 inmates dead in a prison where riots had taken place.
At least 40 police officers, 71 suspected assailants and four passers-by were killed in the four nights of violence, during which 250 attacks were reported.
The First Capital Command, whose leaders operate from prison, launched the attacks on police on Friday in retaliation for the transfer of hundreds of its members to maximum-security prisons.
Sao Paulo, South America's biggest city and Brazil's business centre, has been gripped by fear for three days as the gang burned buses, forcing the shut-down of transport services.
But residents cautiously returned to work on Tuesday and bus services were restored.
Deal denied
Local media reported that the gang's leader ordered an end to the violent campaign after reaching an agreement with state officials.
The newspaper O Estado de Sao Paulo said jailed First Capital Command leader Marcos Cacho, known as "Marcola," had met government officials in prison. But officials denied negotiations had taken place.
"There has been no dialogue with the (gang) leaders to find an accord," state Governor Claudio Lembo said.
Police chief Marco Desgualdo also denied that an agreement was reached with the gang.
"You can't have agreements with criminals," he said, assuring that the bloody offensive was moving toward "stabilisation" and "neutralisation".
Authorities said 115 suspects have been arrested and 113 weapons seized.
Police believe gang bosses were using cell phones from inside the prisons to oversee the unrest.
Meanwhile, order was restored in 73 prisons hit by gang-launched uprisings to coincide with the street attacks, after prison officials negotiated the release of 195 hostages on Monday.
Sao Paulo residents cautiously returned to work on Tuesday, but several schools and universities remained closed, while buses returned to the streets with police escorts.
On Monday, bus service ground to a halt and restaurants and shops also shut down after the gang attacked civilian targets of the first time, torching scores of buses and hurling Molotov cocktails at banks.
"The gangsters do what they want, you would think this is Iraq," said Bety, an east Sao Paulo resident. "It's terrifying.”
The First Capital Command, known by its Portuguese initials PCC, is the largest criminal gang in Sao Paulo state and has a massive base in prisons.
It first emerged in prisons in the 1990s and was responsible for uprisings in 20 penitentiaries in February 2001. In November 2003, it launched attacks on security forces that left 11 officers and seven gang members dead.