The girls, who were 12 at the time, were accused of stabbing Leutner during a birthday party sleepover. Leutner was stabbed 19 times.
Her body was later discovered in a nearby park in Waukesha, a city west of Milwaukee.
Weier's guilty plea comes as her parents revealed their side of the story for the first time this year.
In a TV interview with ABC News in the US, Bill and Kristi Weier said their daughter feels "remorse" and "vents" during visits.
They also revealed details of what Leutner said on the day of the attack.
"Payton stated that she thought Morgan was her friend," Kristi Weier said.
"I pray every day that Payton finds true friendship."
Although their daughter has pleaded guilty to the lesser charge, her court case is not over yet.
She still faces a trial next month focused on her mental health. Her plea means her trial will look at if she is legally responsible for the crime or not guilty because of mental illness.
If she's found guilty, she could face at least 10 years in prison. If not, she'll spend three years in a mental hospital.
Prosecutors allege Weier and Geyser stabbed Leutner 19 times in a park and then planned to walk hundreds of miles north to meet Slenderman in a forest.
Leutner was able to crawl out of the woods to a path where she was found by a cyclist.
Somehow, she miraculously survived the brutal attack, and returned to school one year later.
Leutner previously told ABC's 20/20 she'd feared Slenderman before the attack and tried to back away from the forest because she "sensed something was wrong".
Her mother Stacie told of seeing her daughter in hospital "as pale as a ghost".
"She was crying. She couldn't breathe. She saw me. She put her hand out and I rushed over to her and I put my arms around her and I laid next to her," she said.
Geyser, also due in court for a hearing, pleaded not guilty by reason of mental disease to an attempted homicide charge. Weier initially entered the same plea, before her court appearance today.
Experts have already testified that Geyser suffers from schizophrenia and oppositional defiant disorder and maintains relationships with imaginary characters.
The news comes after filmmakers released an HBO documentary titled Beware the Slenderman, which is based on the attack.
The documentary detailed what happened during the attack and included audio from a 911 call and police footage from inside the interview room as Weier revealed her motive.
"I was really scared knowing that Slenderman could easily kill my whole family in three seconds," she tells an officer.
It is alleged the attack was carefully planned over five months.
Police say the girls told detectives they wanted to murder the girl after reading tales about Slenderman on the horror website CreepyPasta.
Slenderman, the creation of paranormal enthusiasts, is said to be a lanky, faceless character in a suit who terrorises and kidnaps children.
It is believed the spooky figure was invented in a Photoshop contest on the Something Awful forums in 2009 and became the subject of online paranormal fan fiction.
He is also the subject of a number of YouTube mockumentaries where he terrifies viewers by making an appearance at a person's front door.
