The manager, whose name has not been made public, worked in the City Retail unit of the Chinese e-commerce company, which works in the delivery of groceries to supermarkets.
He is accused of committing “intimate acts” with the woman while she was drunk and asleep, according to an internal memo from Alibaba boss Daniel Zhang, published Monday.
The man “has been made redundant and will never be rehired,” he said.
Local police are investigating the incident and two other staff – the president and head of human resources of the City Retail unit – have also resigned over allegations that they have not taken action, says the memo.
The alleged victim posted on Alibaba’s intranet site an 11-page account of what she says happened.
She says the supervisor and a client forced her to drink alcohol on a work trip and sexually assaulted her afterwards.
His post was quickly made public and was among the trending Chinese social media website Weibo over the weekend.
A panel discussion on the alleged incident on Alibaba’s workplace courier service, Dingtalk, had more than 6,000 employees as of Monday morning.
They call for justice and a crackdown on sexual harassment in the workplace.
Mr. Zhang said the company was fiercely opposed to the “ugly culture of forced consumption.”
It will implement a company-wide training program and set up a dedicated channel for people to report incidents, he said.
The chief executive also promised to publish an official zero tolerance policy on harassment and gave his human resources manager a “demerit” on how the case was handled.
Alibaba was founded by retired billionaire Jack Ma in 1999, five years after rival Amazon launched in the United States.
Its Alipay electronic payment service was rolled out five years later.
Mr. Ma was not seen in public for several months last year after criticizing Chinese competition regulators.