The case had caught India between Saudi Arabia, one of its largest oil suppliers, and Nepal, a small neighbour where it is battling with China for influence.
India took the unusual step of naming the diplomat Majed Hassan Ashoor, the first secretary at the Saudi embassy, in a statement late on Wednesday announcing his departure.
Read: Indian village tribunal orders rape of two sisters to punish brother who eloped
The statement said Ashoor was protected under the Vienna Convention on Diplomatic Relations, which grants diplomats immunity from arrest, criminal prosecution and civil lawsuits when they are posted overseas.
The incident posed a challenge for Prime Minister Narendra Modi, who is due to make a rare visit to Saudi Arabia later this year. At the same time he has made improving relations with neighbouring Nepal, one of his top foreign policy priorities.
The Nepali women were rescued from the diplomat's apartment last week after a tip off from a human trafficking group and the Nepalese embassy.
The women told police they were gang raped, assaulted and denied water and food while being captive for several months. The women said they were raped by eight men on one occasion.
Read: India court stops Uber rape accused re-examining witnesses
Both women came from remote rural parts of Nepal and were sent to Saudi Arabia as domestic servants by human traffickers before returning to New Delhi with their employer.
The Saudi Embassy did not respond to Reuters' requests for comment. In an earlier statement, the embassy said the allegations were false.
A police officer involved in the case said he is confident they will be able to track the other accused men because they have CCTV from the entrance of the apartment and will be able to track their mobile phones.
COMMENTS (3)
Comments are moderated and generally will be posted if they are on-topic and not abusive.
For more information, please see our Comments FAQ