The sister had previously claimed she was forcibly married off at age 15 and raped.
The boy was arrested in April after calling the police to tell them he had found his older sister Maria dead in her apartment in Landskrona in southern Sweden.
When formal charges were filed earlier in November, prosecutor Magnus Larsson said that the 17-year-old denied having committed the crime.
The brother claimed Maria was killed by a masked perpetrator.
He also said that his dying sister begged him to call a friend for help, which he did, before then calling police.
But in a packed hearing room at the Lund District Court on Monday, the prosecutor accused the boy of lying, and presented evidence that she could not have expressed her last wishes to him.
"The medical examiner found that her windpipe had been cut. Therefore, she couldn't have spoken with her brother," Larsson told the court.
Just days before her death, she made a recording, which was played in court on Monday.
"When I was 15, I was raped and married off," Maria could be heard saying.
She had been speaking with the women's support group Tänk Om ('Think Again'), which works to combat honour violence. They had given Maria shelter in the months before her death and recorded her claims of abuse.
In the more than 30-minute long tape, she spoke at length about the notion of "family honour" that permeated her upbringing.
She then details being kidnapped and taken abroad as a 12-year-old.
In the recording, she says she fled back to Sweden when she was 15 but was forced to live with threats and harassment.
"She was constantly worried about being murdered. She felt that there were plans being hatched against her, and that fear proved to be justified," Newroz Zeynep Ötunc of Tank Om told the TT news agency.
Maria was found with more than 100 stab wounds to her head, abdomen, back, and neck.
In making his case, prosecutor Larsson pointed to forensic evidence implicating Maria's brother, including cuts on his hands.
The 17-year-old's fingerprints were also found on one of the knives and his sister's blood was found on his clothes.
Police found two knives and a pair of scissors near the victim's body.
"The blade on one of the knives was bent sharply. The bending probably occurred due to stabs to the body," said Larsson, who showed the court several images of blood-stained walls and pools of blood on the floor of Maria's flat.
While police and prosecutors have investigated Maria's murder as an honour killing, they have not found proof that the killing was orchestrated by her family, as alleged by representatives from Tänk Om and others.
"It's possible to prove that Maria lived within an honour culture and that the accused and the rest of the family had opinions about her way of life," Elisabeth Massi Fritz, an attorney representing Maria's sister, told TT.
"It's unfortunate that the prosecutor doesn't see the honour culture problem. My client thinks it's important to highlight it during the proceedings."
Early in the investigation, Maria's mother was also arrested on suspicion that she had a role in the killing. She was later released.
Last week, she told the Aftonbladet newspaper she would "never forgive" her son if it turns out that he killed his sister.