Officers also have three male 'persons of interest', two of whom are now in custody being questioned. The third, named as George Barazza, is believed to have fled to Mexico.
Chavira, now 30, was arrested near her home in Lancaster, California, over the murder, which took place when the pair were living among the Hispanic community in East Los Angeles.
The Los Angeles County District Attorney filed charges of special circumstances of felony murder during the commission of a kidnapping and rape and gang allegations.
LA County police lieutenant Dave Coleman told a press conference: 'She actually was a friend of Brenda at the time and coordinated the kidnap itself, and evidence indicates to us that she was present during the rapes and during the murder.
Because she was 15 years old at the time of the murders, Chavira faces life in prison without parole if she is convicted.
She pleaded not guilty at an initial hearing.
Brenda was walking to a friend's house on her way to Schurr High School when she was abducted in the street at 7.30am on October 18, 2002.
Her body was discovered the next day in the Valley of Enchantment area of the City of Crestline, in San Bernardino County.
The San Bernardino Sheriff’s Department investigated the brutal murder for six years before it was passed over to the detectives of Los Angeles County.
Despite the offer of a $150,000 reward and the release of composite sketches of two male suspects in 2012, an arrest was never made.
But detectives persisted with the case, using new DNA technology, surveillance footage, witnesses and clues from gang members who had relinquished their criminal past.
Officers now believe they have a timeline for Brenda's final hours.
They say she was kidnapped in the area of Whittier Boulevard and Leonard Avenue in East Los Angeles.
She was taken to a home in nearby Williamson Avenue, where she was sexually assaulted.
She was then moved again to another home in Miller Avenue, where she was bludgeoned to death. Her body was later transported out of the city.
Witnesses saw a 'suspicious, dark, SUV' in the area where her body was found, while other witnesses near Brenda's home saw 'one or two females' talking to her in the street.
The case is another agonising twist for Brenda's mother Fabiola, who has waited 13 years for answers over her daughter's senseless murder.
An LA County police spokesman claimed the force has 'worked tirelessly to bring her killers to justice'. They are still looking for outstanding witnesses.
Lt Coleman said: 'We hope that anyone with knowledge of this horrific incident will overcome any fear of coercion or retaliation and come forward and bring justice to Brenda and her family.'
Read more: http://www.dailymail.co.uk/news/article-2978902/Breakthrough-murder-15-year-old-snatched-way-school-LA-2002-woman-15-time-arrested.html#ixzz57gATmz1I
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