Huong did not react to the ruling, but Siti Aisyah burst into tears and had to be comforted by her lawyers and officials of the Indonesian embassy.
The judge the prosecution during the six-month trial so far had laid out enough evidence of the women's guilt for the case against them to proceed.
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.
"It can not be said that the prosecution has produced credible evidence to establish a prima facie case", said Hisyam.
"I must therefore call upon them to enter their defence on their respective charges", he said. Defence lawyers said the real culprits had left the country at a hearing a year ago.
Kim Jong-nam died at Kuala Lumpur's airport previous year after the toxic VX nerve agent was rubbed on his face. He said, "I had thought she would be innocent".
"We will also support Siti fully throughout her defence trial with existing resources available to us", he said when met at the side after the verdict.
Prosecutors allege that Doan's behavior after the incident - security footage shows her rushing to the washroom with her hands held away from her body - indicates that she was, in fact, aware of handling a risky substance.
If the judge decides the evidence is insufficient, the case will be dismissed and both women acquitted and deported.
Indonesian Siti Aisyah, who is on trial for the killing of Kim Jong-nam, the estranged half-brother of North Korea's leader, is escorted as she arrives at the Shah Alam High Court on the outskirts of Kuala Lumpur, Malaysia on August 16, 2018.
Malaysia cancels a visa-free travel deal with North Korea and deports North Korea s ambassador. The pair, who are the only suspects in custody in connection with the killing by poison, face a mandatory death sentence if convicted.
The killing took place more than five years after Kim Jong Un took power, when tensions between North Korea and the worldwide community were high. However, he suggested the prosecution's case had been weakened by its sole reliance on security footage and its failure to call any witnesses to the stand. Vietnamese suspect Doan Thi Huong has also told the court she intends to testify, but it's not immediately clear when she will do so.
Kim had been living in exile with his family in the Chinese territory of Macau.
The message was delivered to the North's leader as Putin congratulated North Korea on the 73rd anniversary of Korea's liberation from Japan's 1910-45 colonial rule, according to the Korean Central News Agency (KCNA).