In a letter shared by Huong's lawyers ahead of her departure from Kuala Lumpur, Huong thanked the governments of Vietnam and Malaysia for their support.
Lawyers for the two women argued they were duped by North Korean agents who tricked them into thinking they were taking part in a prank reality TV show.
She pleaded guilty to the lesser offence of voluntarily causing injury with a unsafe weapon instead of the original charge of murder, which in Malaysia carries a mandatory death penalty.
More than two years after her arrest, the 30-year-old was freed from prison in the early morning, racing past journalists in a van with heavily tinted windows.
Malaysian officials have said that the North Koreans who were believed to be suspects in Kim Jong Nam's killing left the country hours later.
Four North Koreans are named as co-conspirators in the 2017 killing of Kim, but they escaped to North Korea.
"I'm very happy, thank you all a lot", Huong said in a message read by her lawyers.
"Thank you Lord Jesus for the love (showered) on me", the message said.
Vietnam then stepped up pressure for Huong's murder charge to be dropped and at the start of April, prosecutors offered her the lesser charge, paving the way for her release.
Huong's lawyer, Hisyam Teh Poh Teik, told reporters at the airport that "the case has come to a complete end" because prosecutors didn't file any appeal of the sentence given Huong.
Aisyah and Huong were put on trial for murder in October 2017 and faced death by hanging if convicted.
The four enigmatic North Korean agents thought to have staged the murder fled Malaysia immediately afterward and have never been found, despite a "red notice" global warrant from Interpol.
A prision security officer stands guard as members of the media await the release of Vietnamese Doan Thi Huong from a prison in Kajang, Malaysia, May 3, 2019. South Korean and US officials have talked about the involvement of North Korea, ruled by Kim Jong Un (left), in murdering the half-brother of the leader, Kim Jong Nam (right).
The assassination plot: The prosecution failed to show the women had any intention to kill.
Ties have improved in recent times, however, with Malaysia saying it plans to reopen its embassy in Pyongyang, which was closed shortly after the murder.