In her dismissal letter, she was accused of spreading falsehoods that damaged the company's reputation.
In August, the employee made her claims public because Alibaba failed to act. The assaults occurred on a business trip, she claimed.
The colleague was fired, but the criminal case against him was dropped.
Police are still investigating the client.
This case is well-publicized and highlights the harassment of women at work in China.
According to the government-backed newspaper Dahe Daily, she was fired in late October. It published a copy her termination letter.
In the letter, she claimed that she had made false statements about the assault and that the company was not handling the case.
This "caused severe social concern and had a negative impact on the company", it added.
According to the employee, he stated that he had not committed any errors and would not accept this outcome. He also said that he would use legal remedies in the future to protect his rights and interests.
Lawyer for the woman confirmed her dismissal to The New York Times.
Alibaba, China's largest online retailer, didn't immediately respond to a BBC request for comment.
What are the allegations?
The eleven-page report by the woman describing the incident included her account that the colleague raped the victim in a hotel room after she had drunk the night before.
It caused a social media storm in China's Twitter-like Weibo.
According to the woman, the colleague in higher management in the company coerced her to travel to Jinan, which is approximately 900km (560 mi) from Alibaba's Hangzhou headquarters, in order for her to meet with a client.
She claimed that her superiors ordered her to have alcohol with coworkers at dinner.
She claimed that the client had kissed her on 27 July. The next morning, she woke up in her hotel room without her clothes on. She had no memory of what happened the night before.
According to the woman, she had surveillance camera footage that showed her co-worker entering her bedroom four times in the evening.
The woman returned to Hangzhou and stated that the incident had been reported to Alibaba's Human Resources (HR) department. She also claimed that she had asked for the firing of the coworker.
She stated that although human resources initially accepted the request, they did not take any further action.
What was the response?
Alibaba was subject to a fierce public backlash and later fired the coworker, identified as Mr Wang. Two executives from the company who failed to respond to the allegation were also fired by Alibaba.
An email was sent out stating that Alibaba was "staunchly opposed" to forced drinking culture.
Alibaba previously stated that the man accused of the rape had confessed to "intimate acts" while the woman "was inebriated".
Although the case against Mr Wang will not proceed, the court has approved the arrest of the client accused of assaulting the victim. His surname is Zhang.
His company also fired Mr Zhang, according to reports.
Online opinion has split on the case. Social media users have posted opinions ranging from that the coworker was too easy to get away with, to others saying there wasn't enough evidence.
This new development is likely spark similar discussions in China, which is currently grappling with the #MeToo movement.
