Siti was one of two women charged with the murder of Kim Jong-nam in Kuala Lumpur airport in February 2017. Both Aisyah and Huong have said that they believed they were taking part in a prank for a television show, and thought they were applying lotion on the man's face.
"I am very happy, I never expected that today I will be freed", she said at a press conference with representatives of the Indonesian government in Kuala Lumpur on Monday, which was aired live by Kompas TV.
"I thank our president Mr. Jokowi, and all ministers who have made efforts to help me and bring me back to Indonesia", she said.
Earlier on Monday as the court resumed the trial, six months after a judge ruled there was sufficient evidence for their involvement in the murder, prosecutor Muhammad Iskandar Ahmad requested that the murder charge against Aisyah be withdrawn and that she be given a discharge.
Siti Aisyah had been working as a masseuse in Kuala Lumpur, while Doan described herself as an entertainer.
The judge discharged Siti Aisyah after prosecutors said they wanted to withdraw the charge.
Indonesian Siti Aisyah flew to Jakarta on a special aircraft arranged by the Indonesian embassy in Kuala Lumpur. While some reports state that due to this surprise development, Doan's trial has been put on hold, others state that her trial will take place this Thursday (14th March). She later tearfully told reporters that she was "shocked" to have been freed after more than two years behind bars.
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He said Aisyah was free to leave the country.
Malaysia expelled North Korea's envoy for questioning the government's impartiality in handing the murder investigation, and North Korea retaliated with a travel ban on all Malaysians in Pyongyang, trapping three diplomats and six family members.
Salim Bashir, a lawyer for Huong, said previously she was prepared to testify under oath for her defense. They were the only suspects in custody after four North Korean suspects fled the country on the morning Kim was killed.
"We truly believe she's a scapegoat and she is innocent as we laid out [before]", he said.
The defense had disputed whether the CCTV footage was clear enough to identify the Indonesian woman as an assailant, or establish what she had done to the victim.
A murder conviction carries a mandatory penalty of death in Malaysia.
But lawyers have consistently argued that they were merely used for the political assassination, which had clear links to North Korea.
Mr Kim had been living overseas for years but could have been seen as a threat to his half-brother's rule.