The spate of attacks in Brazil's largest city in August left seven dead and shocked the country. Eight more victims remain in hospital.
The arrested men, Marcos Martins Garcia and Jayner Aurelio Porfirio, have already been detained for more than a month and can be held until 15 November when charges must be brought.
A third man, described as "clandestine security", is also being held.
On 19 October, groups representing the homeless held a march to mark two months since the attacks, which were carried out over two days in the centre of the city.
Protesters gathered on the steps of the historical Se Cathedral to mark the spot where many of the homeless were murdered.
The killing spree was marked by its brutality, with victims allegedly beaten on the face and head with wooden clubs.
The seventh man died from his injuries after three weeks in
hospital. President Luiz Inacio Lula da Silva has condemned the incidents as "barbarous crimes which smell of prejudice".
The police homicide department says it believes the killings were carried out by men commanding a private security and drug trafficking operation in the centre of the city.
"There is a practice of genocidal war against poor people. To kill a human being with a wooden club shows that we live in a savage society"
Professor Robert Romano,
State University of Campinas
Secretary of Security Saulo de Castro Abreu Filho said the attacks were possibly provoked by an influx of drugs into the city centre.
"We need to find the root of the problem," says Julio Lancelloti, vicar to the street people.
"There are organised crime and underground security groups, it's not just two or four people.
"We are reunited, one more time, in the name of peace. We are remembering a series of attacks and the lack of solutions for the massacre and we don't know how it will end."
Brazil's secretary of human rights has called for an inquiry into illegal private security groups in the centre, while Justice Minister Marcos Thomasz Bastos has promised that "justice will be done in this case".
Police initially blamed the attacks on a turf war between the 10,000 homeless people in Sao Paulo. They dismissed the testimonies of survivors as unreliable.
None of the images from dozens of CCTV cameras around the area of the attacks has been released.
As Aljazeera.net reported days after the attacks, the street community suspected police involvement from the start.
Police initially blamed the attacks
on a turf war among the homeless
"Here in the centre it is well policed, but not for us, the people of the street," says Anderson, who is homeless.
"When we call for help from the police, they ignore us or they beat us. They aren't here for our safety."
Thousands slept out in the streets declaring that "if the military police are not going to protect the homeless, we are going to do it ourselves".
The attacks have reminded people of the infamous Candelaria massacre of street children by off-duty police in Rio de Janeiro in 1993.
One theory is that the second day of killings was targeted at those who may have witnessed the first.
Another says that one man was specifically targeted and the rest murdered to confuse any investigation. The homeless may also have known that the police were involved in drug trafficking and were killed to "burn the files".
Spotlight on homeless
The murders have shone a spotlight on the situation of the homeless like never before. Brazil's media now routinely record attacks on street people, not just in Sao Paulo but in cities across the country.
An amateur video shot of three men dragging a homeless man into the road in Rio and stuffing paper into his jacket - as if to prepare to burn him alive - was shown on Brazil's biggest nightly news programme, Journal Nacional.
"We need to find the root of the problem. There are organised crime and underground security groups"
Julio Lancelloti, vicar to the street people
Further south in the state of Parana it was reported that a 41-year-old homeless man, Severino Dantas, was doused with alcohol and set on fire earlier this month. He survived with 60% burns to his body.
Before the Sao Paulo attacks the homeless were almost invisible, their deaths just one more statistics - if recorded at all.
Brazil is one of the most violent countries in the world with murder rates higher than many war zones. Almost 600,000 people have been murdered in the past 20 years - an average of 82 a day.
Mayor Marta Suplicy (L) and Lula
are not immune to the issue
"There exists an insupportable ethic in Brazilian society that needs to urgently change," says Robert Romano, a professor at the State University of Campinas.
"There is a practice of genocidal war against poor people.
"To kill a human being with a wooden club shows that we live in a savage society."
The question of homelessness has also become a political
battleground, with the attacks coming in the middle of the election for Sao Paulo's mayor - the most important vote after that for president and one that is being seen as a test for President Lula.