However, according to a detailed report in Brazilian newspaper Band B, Freitas had been the victim of "torture".
Quoting a municipal guard, the report stated: "From the appearance of the body, it was a very violent situation.
"The man had two deep cuts on his neck, was nearly beheaded, and his genitals were severed."
The body was found by people walking around the area.
The report further claimed that the road where Freitas' body was found is known for the spawning of corpses.
"Everything indicates the man was executed here on the street and dragged for about 30 metres," the report states.
Freitas began his career at Cruzeiro and played for Botafogo for two years before signing for six-time Brazilian league winners Sao Paulo in 2015.
The attacking midfielder, however, was loaned to other second-tier Brazilian outfits after he failed to impress consistently.
Freitas spent the first half of 2018 at Ponte Preta but failed to turn out for the club, while he made only three appearances during a seven-month loan at Coritiba in 2017.
Sao Paulo said in a statement that they "lament the passing of Daniel and offer their support to his friends and family in this moment of suffering".
Sao Bento said the club "stands in solidarity with the family and friends of the player in the time of profound sadness".
No arrests have been made.
