"Yes, I want to plead guilty. I wanted from the first moment to confess sincerely," he told the panel of three judges that will decide his fate, hoping for a reduced sentence. "I truly am sorry for this act. I feel very bad."
Prosecutors are asking for a 30-year prison sentence under charges that carry a 15-year minimum.
The 24-year-old Dutch citizen did not show emotion during his brief confession in fractured Spanish and did not call on the services of a Dutch translator provided for the proceeding.
He bowed his head later when his lawyer, Jose Jimenez, argued that he killed Stephany Flores, 21, as a result of "extreme psychological trauma" he suffered from being "persecuted" over the disappearance of Natalee Holloway on the Caribbean island of Aruba, "something he says he never did and for which no evidence at all exists."
He said judges, in sentencing, should consider the "post-traumatic stress" his client suffered.
Conferring privately with Jimenez before leaving the courtroom, Van der Sloot briefly smiled.
The judges have 48 hours to render a sentence and the presiding magistrate, Victoria Montoya, said it would reconvene Friday to do so.
Van der Sloot's trial opened last week but was adjourned to Wednesday after he asked for more time to decide how to plead. He said then that he was inclined to confess but did not accept the aggravated murder charges the prosecution sought.
Van der Sloot, who wore faded jeans and an untucked light-blue button-down shirt, had confessed to the May 30, 2010, killing long ago.
He told police shortly after the murder that he killed Flores in a fit of rage after she discovered his connection to the disappearance of Holloway on his laptop while they played poker online. His lawyer argues it was manslaughter, for which the minimum sentence is 5 years.
Police forensic experts disputed that claim and the attorney for the victim's family contends Van der Sloot killed Flores, a business student from a prominent family, in order to rob her.
Prosecutors charged him with first-degree murder and theft.
The prosecution maintained Van der Sloot killed Flores with "ferocity" and "cruelty," beating then strangling her with his bare hands in his Lima hotel room, concealing the crime and fleeing to Chile, where he was caught two days after Flores' rotting body was found in his hotel room.
Prosecutors say he took more than $200 in cash plus credit cards from the victim and made his initial getaway in her car, leaving it in a different part of Lima.
The length of the sentence is completely at the judges' discretion, said court officials and a leading Peruvian criminal attorney, Luis Lamas.
The attorney for the family of the victim, Edwar Alvarez, has argued for life in prison and deemed a sentence reduction "unacceptable."
"In the court record, this man has submitted to psychological examinations and they have concluded that he is a psychopathic person," he told reporters. "What judge would give a psychopath a penal benefit?"
The victim's father, circus impresario and former race car driver Ricardo Flores, attended the opening of the trial but not Wednesday's hearing.
Reached by phone before Van der Sloot's plea, he said he could not bear to even watch the proceedings on TV.
"There is nothing in the is matter hurts us," he told The Associated Press.
Ricardo Flores told the AP Friday said the family, as a party to the trial, had planned to introduce testimony from friends of his daughter and casino employees proving that she won $10,000 there and that Van der Sloot had learned of it. He said the casino had videotape of his daughter cashing in the chips.
Video taken at the Atlantic City Casino where the victim met Van der Sloot shows the two leaving together, and closed-circuit images from the downmarket TAC hotel shows the pair entering together and Van der Sloot leaving alone hours later, bags packed.
After strangling Flores, Van der Sloot left the hotel room and, to hide the crime, bought two cups of coffee across the street, asking a hotel employee to open his room when he returned, Prosecutor Jose Santiesteban said in the trial's opening argument Friday.
Van der Sloot continues to be dogged by the case of Holloway, a Mountain Brook, Alabama, 19-year-old who disappeared during a high school graduation trip in 2005 to the Dutch Caribbean island of Aruba where Van der Sloot grew up.
She was last seen leaving a nightclub with him. Her body has never been found.
The case received a storm of media attention and the tall, garrulous Dutchman became a staple of true-crime TV shows, in several interviews describing himself as a pathological liar. In a clandestinely taped conversation, he is seen telling a Dutch TV reporter he was involved in Holloway's disappearance.
Van der Sloot's trip to Lima may have been funded by continued fallout from that case.
U.S. officials, who indicted him on extortion and fraud charges days after the Flores killing, say Van der Sloot had just extorted $25,000 from Holloway's mother, Beth Holloway Twitty, by offering to lead her attorney, John Q. Kelly, to Holloway's body in Aruba.
After meeting with Kelly there, without delivering on his offer, he flew to Lima on May 14, 2010, they say. Two weeks later, Flores was killed.
Ricardo Flores said he doesn't think Van der Sloot is contrite over his daughter's death and wants the defendant placed in conditions of greater deprivation.
That could include being extradited to the United States to stand trial there once he's been sentenced in Peru.
In a statement issued Wednesday, Kelly said that after Van der Sloot is sentenced "we anticipate that U.S. authorities will move quickly to bring him to Alabama to face pending federal charges, and to answer for his past conduct in Aruba."
Peru's Foreign Ministry says it has no U.S. extradition request for Van der Sloot.
U.S. authorities have requested his arrest through Interpol "should he be released on the charges there" so he could be brought to Alabama, for trial, said Peggy Sanford, a spokeswoman the U.S. Attorney's office in Birmingham, Ala.
No members of Van der Sloot's family have attended the trial.
His lawyer said his client's mother, Anita, did not want the media attention. The defendant's father, a prominent lawyer, died of a heart attack at age 57 in February 2010.
