The 22-year-old, known only as Laura, flew out of Doha on Wednesday night, Dutch foreign ministry spokeswoman Daphne Kerremans said.
"I confirm her departure and she's back in the Netherlands," Kerremans said.
A KLM air hostess only identified as "Audrey" told DJ Giel Beelen on Dutch public radio 3FM that she was on the same flight as the woman.
"She wasn’t alone, she travelled with a female companion," the air hostess said.
"Just before we landed we were informed that she was on board," she said, adding that she was "taken to the front to business class ahead of the landing".
A court in Doha on Monday handed the woman a one-year suspended prison sentence. Court officials said at the time that she would be deported after paying a fine of 3,000 Qatari riyals ($800/710 euros).
The woman, who was in Qatar as a tourist, was arrested on March 14 and held in custody.
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She denied the charge against her, saying she had been drugged and raped after visiting a bar at a Doha hotel.
"Laura went dancing but when she returned to the table after the first sip of her drink, she realised that" she had been drugged, her lawyer Brian Lokollo has said.
Lokollo added that the woman remembered little until the following morning when she woke up in a totally unfamiliar apartment "and realised to her great horror, that she had been raped".
However, the Syrian male defendant, Omar Abdullah al-Hasan, insisted that their night together had been consensual and that the woman had even asked for money.
On Monday, he was sentenced to 100 lashes for having illicit sex and 40 lashes for drinking alcohol.
Adultery, or illicit sex, is treated as a serious crime in the conservative emirate.
The case highlighted the cultural sensitives between Qatar, which will host the 2022 football World Cup, and its many Western visitors.
It received little attention inside Qatar but prompted an international outcry with many people appalled by the treatment of an alleged rape victim.
An online campaign using the #freelaura hashtag to try to draw attention to the Dutch woman's detention was also launched.