The decision was a blow to the suspects' families who insist the pair were tricked into carrying out the dramatic hit.
After hearing the prosecution case, the judge said there was sufficient evidence to support a murder charge against Siti Aisyah from Indonesia and Doan Thi Huong from Vietnam, accused of assassinating Kim Jong Nam, the half-brother of North Korea's leader, with nerve agent VX at Kuala Lumpur airport.
Judge Azmi Ariffin said the evidence presented in court since the trial started in October pointed to a "well-planned conspiracy" with a group of North Korean suspects who are still at large.
"I must therefore call upon (the suspects) to enter their defence on their respective charges," he said in his ruling to the Shah Alam High Court, outside Kuala Lumpur.
The women, who are set to testify during the defense stage of the trial, looked shocked and tearful as the ruling was handed down. The judge could have chosen to acquit the women if he thought the evidence was insufficient.
Their families insist the pair were tricked into carrying out the Cold War-style killing, and had been hopeful they would be acquitted, although state prosecutors insisted they had a strong case.
'She was fooled'
"She knows nothing, she was fooled. The case (against her) was made up," Aisyah's father, Asria, told AFP from the family's village on Indonesia's Java island.
Her mother Benah added: "This is unfair. I wanted her to be released today but if the court refuses what can I do? I can only pray for the final verdict."
The women are accused of killing Kim Jong Nam -- once seen as an heir to the North Korean leadership and a rival to current leader Kim Jong Un -- by smearing toxic VX on his face in February last year as he waited to board a flight to Macau.
The pair, who could face death by hanging if found guilty, claim they fell victim to an elaborate plot hatched by North Korean agents and believed they were taking part in a prank for a reality TV show.
But prosecutors, who likened the murder to the goings on in a "James Bond" movie, argued the pair were well-trained assassins who knew exactly what they were doing.
During months of hearings, the court has been told that four North Koreans -- who are formally accused alongside the women -- recruited the pair and were the masterminds, providing them with the poison on the day of the murder before fleeing the country.
'Deeply disappointed'
CCTV footage seen in court during the trial showed the women rushing to separate bathrooms in the airport after the murder, before leaving in taxis.
In his ruling, the judge said that the footage "showed that they had the knowledge that the liquid on their hands was toxic."
The defence teams have argued the women are simply scapegoats, with the authorities unable to catch the real killers and therefore desperate to secure some kind of conviction in the case.
Despite the evidence against them, the women's lawyers believed that prosecutors had not shown they intended to kill Kim, who had been living in exile for a decade since falling out of favour with the North's ruling family.
"We are deeply disappointed with the ruling... We will do our best at the defence stage," said Aisyah's lawyer Gooi Soon Seng.