The girl told her mother and the police were called in the morning.
Aware that police wanted to speak to him, he told his current partner to tell police that he had been at home with her that night.
When spoken to by police, he denied the offences and claimed he was with his girlfriend all night.
His partner later retracted the false statement.
Analysis of Fowler's cellphone data showed that between 2am and 5am, his cellphone was located in the area of the girl's house, and not where he said he'd been.
DNA testing also linked him to the crimes.
Fowler, a machine operator of the Christchurch suburb of Phillipstown, earlier admitted eight charges, including two counts of rape, two of sexual violation by unlawful sexual connection, attempted sexual violation, sexual conduct with a young person, burglary with a weapon, and attempting to pervert the course of justice.
The girl, now 16, had a harrowing victim impact statement read aloud in court today.
She spoke of her anger at what had happened, and how it had greatly changed her life.
She had been a popular, above-average student who enjoyed learning, felt positive about her future and "believed I could do anything I wanted".
After the first sexual assault, she went to school the next morning "as if nothing had happened".
"I guess I was too young to understand," she said.
The second attack left her "scared and disgusted".
Now, she doesn't believe that she will ever get over it.
Her school work has suffered, she has lost motivation and focus, and failed her last exams.
She has started smoking, has trouble sleeping, and suffers recurring nightmares of the assault which replays what happened "frame by frame".
She doesn't leave home unless she has to and is now scared and untrusting of men.
"I feel he has taken away my strength and dignity."
Justice Rachel Dunningham praised her for a great job in writing the powerful victim impact statement.
Defence counsel Serina Bailey pointed out Fowler had undergone immense difficulties in his own life, but admitted it was no excuse for what he had done.
The judge accepted his upbringing was as traumatic as she had ever seen in reports before the courts.
The Crown suggested that preventive detention was an appropriate sentence for the court to consider.
Two health assessor reports put Fowler at a high risk of reoffending of young girls.
Crown prosecutor Claire Boshier said the second assault at knife point was at the high end of serious sexual offending.
The crime was aggravated by the facts it involved a home invasion, planning and premeditation, and involved a vulnerable young victim.
While there had been 18 years between previous sexual offending, Fowler's high risk of reoffending appeared "ingrained in various aspects of his personality" according to reports by a psychologist and a psychiatrist.
Justice Dunningham noted that Fowler has a limited level of empathy, and therefore remorse, for the victim.
However, she didn't believe that his crimes met the level required for a sentence of preventive detention.
She sentenced Fowler to 12 years, nine months imprisonment with a minimum non-parole period of six years and six months. He has also been placed on the sex offenders register.
