Commissioner Charles Ramsey said he made the decision based on the fact that the man's head and face injuries were not life-threatening, his determination that the neighbors' intent was to bring the man to police and the high level of emotion in the community after the girl's brutal attack.
About a dozen residents of the city's West Kensington neighborhood pummeled 26-year-old Jose Carrasquillo for several minutes on Tuesday. Officers arrived and took him into custody on an outstanding warrant; he has been upgraded to stable condition.
"From what I've seen so far, we have one victim and that's an 11-year-old girl," Ramsey said in an interview with The Associated Press.
Before making his decision, Ramsey said, he monitored Carrasquillo's condition and reviewed surveillance video of the assault. As soon as officers arrived at the scene, he said, the group stopped the beating.
"These people saw him, he attempted to run and they caught up with him," Ramsey said. "If the injuries had been severe, maybe we'd have to rethink it."
The Philadelphia chapter of the Fraternal Order of Police had offered a $10,000 reward in the rape case.
Carrasquillo was released from the hospital Thursday and is in police custody, but has not been charged in the rape, police said.
Ramsey said investigators have very strong forensic evidence and witness identification placing him at the scene. He is also under investigation in connection with two other sexual assaults, Ramsey said.
"I think you have to take into account the emotion. I think you have to take into account the severity of the injuries," Ramsey said, adding that he does not condone vigilante justice. "It's unfortunate that we didn't find him first."
But an attorney for the American Civil Liberties Union said she thought the commissioner's decision not to file charges against the neighbors sent the wrong message to the community.
"It's shocking that the police are not going to do anything in response to what is essentially mob violence against this guy," said ACLU attorney Mary Catherine Roper. "This went beyond apprehending the guy."
The girl had just dropped off a sibling at day care and was walking to school Monday when a man approached her, investigators said. He started to walk with her, threatened her and said he had a gun. He took her to a nearby backyard and raped her repeatedly, authorities said.
A day later, after police had handed out photos identifying Carrasquillo as a "person of interest," neighbors spotted him on the street.
Surveillance video shows a man being chased by at least three people, one of whom hits him several times with what appears to be a bat or large stick. As they chase the man, a crowd gathers. The video cuts off after a police officer arrives.
Ramsey said he had to walk a fine line in deciding whether to charge the man's attackers.
"There is something called a citizen's arrest," Ramsey said. "These are people that aren't trained. They are holding people for police to arrive."
A message left at the public defender's office, which has represented Carrasquillo in prior cases, was not immediately returned Thursday.
FOP president John McNesby did not immediately return a telephone message seeking information on who would get the reward money.