Doan Thi Huong expressed her gratitude "to everybody who prayed for me" in a video taken by her lawyer in the plane just before it took off.
"I want to say I love you all. I thank you my Lord Jesus. Thank you so much," she said.
Huong's release likely closes the case, since four North Koreans named as co-conspirators in the 2017 slaying of Kim Jong Nam using VX nerve agent are not in custody. Malaysian officials never officially accused North Korea of involvement and made it clear they didn't want the trial politicized.
Huong was the last suspect in custody after the Malaysian attorney general's stunning decision in March to drop a murder case against her co-defendant, Indonesian Siti Aisyah, following high-level lobbying from Jakarta. Huong sought to be acquitted after Aisyah was freed, but prosecutors rejected her request. Aisyah returned home to Indonesia.
The two women were charged with colluding with the four North Koreans to murder Kim, North Korean leader Kim Jong Un's elder half brother. The women smeared the nerve agent on his face in a busy Kuala Lumpur airport terminal on Feb. 13, 2017, and have said they thought they were taking part in a harmless prank for a TV show.
Huong, 30, pleaded guilty to a lesser charge of causing injury last month after prosecutors dropped a murder charge against her. She was sentenced to 40 months in prison from the day of her arrest and was released early for good behavior.
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.
Hisyam read out a letter of gratitude in which Huong thanked the Malaysian and Vietnamese governments.
"Thank you Lord Jesus for he loves me so much. I am very happy and thank you all a lot. I love you all," she scribbled in the letter, shown to reporters.
After arriving in Hanoi, Huong said she wasn't sure what she wants to do next, "but I think I want to become an actor."
"What scared me the most when I was in prison was the loneliness and homesickness," she said. "My condition in the prison was good. They did not treat me badly."
The High Court judge last August had found there was enough evidence to infer that Aisyah, Huong and the four North Koreans engaged in a "well-planned conspiracy" to kill Kim and had called on the two women to present their defense.
The four North Koreans left Malaysia the day Kim was killed.
Lawyers for the women have said 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. Intent to kill is crucial to a murder charge under Malaysian law.
Kim Jong Nam was the eldest son in the current generation of North Korea's ruling family. He had been living abroad for years but could have been seen as a threat to Kim Jong Un's rule.