The ruling leaves Ms Doan, who arrived with armed guards at the Shah Alam court shortly before 9am and wearing a bulletproof vest, as the sole suspect in the case still behind bars.
Lawyers for the women argued that they were pawns in a political assassination with clear links to the North Korean Embassy in Kuala Lumpur, and that the prosecution failed to show the women had any intention to kill.
Doan Thi Huong, 30, in bullet-proof attire, was brought to the hospital under heavy guard in a van of the Prisons Department at 9.20 am and left at 10.40 am, said her lawyer, Salim Bashir.
The decision to move forward with Huong's case was slammed by both her lawyer and Vietnam's ambassador, who had hoped she would be given the same leniency as Aisyah.
Vietnam's foreign ministry said it regretted the Malaysian court's decision not to immediately free Huong.
Vietnam's government said earlier that Foreign Minister Pham Binh Binh had asked Malaysia to "ensure a fair trial for Huong and set her free".
He also sought a deferment of the trial, saying Huong has been unwell since Aisyah's release and is not in a position to testify.
The judge agreed to delay the trial until April 1, but warned there should not be any more delays after that.
Prosecutors did not give any reason for the remarkable retreat in their case against Aisyah, but the timing raised eyebrows in Malaysia as a High Court judge had just last August found there was enough evidence to infer that Aisyah, 26, and Huong, 29, had engaged in a "well-planned conspiracy" to kill Kim.
But his daughter is still in custody after a Malaysian prosecutor said Thursday Doan Thi Huong would remain on trial for the gruesome murder of Kim Jong Nam with a toxic nerve agent at a busy Kuala Lumpur airport in 2017.
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She soon gained a large following on social media for her work, and the movement she started spread to other countries across Europe and around the world.
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I think that we played a very, very good first half. "You know very well my relationship with the city, with the people". He can become one of the best in Europe'. "He has been able to train after the problem with the back".
She has been on trial for a year and a half over the 2017 assassination of Kim Jong Nam at Kuala Lumpur airport that shocked the world.
Her lawyers said while she was happy that Siti Aisyah had been released, she was now feeling depressed and had slept for no more than an hour over the past three nights.
'Both the accused have said they were made scapegoats by North Korea, both of them said they were doing video pranks - very obviously there is discrimination, ' said Hisyam Teh Poh Teik. "I have no idea what is going on", she said. Under Malaysian law, intent to kill is critical to a murder charge. The defense part of the trial was to have started Monday.
Oh said Vietnam, which hosted North Korean leader Kim Jong Un for an official visit and a summit with President Donald Trump last month, had pushed less hard for Huong.
"It's so unfair. They were together, did the same thing", she said.
Both women were facing murder charges over the death of Kim Jong-nam.
During the trial, the court saw airport CCTV footage showing Huong approaching Kim, placing her hands on his face and then running away.
The defence phase of the trial is expected to shift the focus onto the absent North Koreans.
On Malaysia's request, Interpol has issued arrest warrant for the four men, who are believed to be back in Pyongyang, but North Korea is not a member of the organisation.