Pictures of the pair severely bruised and injured went viral online, and led to widespread condemnation of the Taliban’s treatment of journalists in the wake of their takeover of Afghanistan.
Mr Naqdi told SBS News he has since lost some hearing in one ear and sight in one eye as a result of the assault.
"My eardrum has burst, my doctor confirmed this, [and] I can’t hear too well on my left ear," the 28-year-old said. "My doctor also said I've lost 40 per cent of my vision in one eye.”
He said while he was covering the protest, a Taliban fighter told him he’d be shot if he continued.
“I said it was important I cover a protest about women raising their voices," he said.
At the police station where he said Taliban fighters later took him and his colleague, he heard screams coming from other rooms.
That's when the beating began, he said.
“They took me to an empty room, and one of the Talibs took their scarf off and tied my hands, took my phone off me and demanded I sit on the floor," he said.
“My hands were tied, my feet were tied. They kept hitting me on top of my head, behind my head, and I was trying to get up to explain I was just a journalist and I did nothing wrong, and they should not be doing this. They didn’t listen.
“I thought this was the end of my life. They had no mercy. I was terrified.”
Mr Naqdi said he fell unconscious repeatedly throughout the four-hour ordeal and remembers shaking uncontrollably and vomiting when he awoke.
When he and his colleague were released from custody he went outside and was warned by another Taliban member their ordeal could have been worse.
“He said: ‘Be thankful, because if it was me, I would have slit your throat',” Mr Naqdi said.
It’s now been almost a month and Mr Nadqi has not returned to work. He says the future of journalism in his country is bleak and he fears being killed if he goes back to doing his job.
Mr Naqdi this week applied for an Australian humanitarian refugee visa along with 12 of his colleagues, including Etilaatroz editor-in-chief Zaki Daryabi.
Australia’s union for journalists, the Media, Entertainment and Arts Alliance, has thrown its support behind their asylum bid.
MEAA president Marcus Strom said the union held grave concerns for the safety of the Etilaatroz staff.
“This newspaper has bravely and fearlessly campaigned against corruption in the former government and among Taliban commanders,” Mr Strom said.
“Etilaatroz journalists have exposed Taliban atrocities and war crimes for almost a decade but its journalists are now at serious risk of arrest, detention and torture while they remain in Afghanistan.
“It would be a strong gesture of support for the principles of press freedom if the Australian government was to accept any applications for resettlement by the journalists.”
Afghan reporters plead with the Australian government to grant them asylum
Hundreds of journalists working in Afghanistan are believed to have recently fled the country or gone into hiding, according to the International Federation of Journalists, which estimates more than 153 media outlets have been forced to close amid the Taliban takeover.
Fears are also growing for the fate of photojournalist Morteza Samadi, who, like the Etilaaroz journalists, was also detained by the Taliban after covering the women's protests on 7 September. He has not been heard from since his arrest.
Australian journalist Peter Greste, a former Afghanistan correspondent who was jailed in Egypt for over a year, said the future of journalism in the country looked “terrible”.
“The beating of the two Etilaatroz journalists tells you pretty much all you need to know about the situation facing journalists across Afghanistan,” he said.
“Whatever the (Taliban) might say in public at the moment, Afghan journalists understand very, very well, just how much danger they're in - a lot of them are in hiding, a lot of them are running, and moving from house to house ... because they are terrified of being caught and beaten, or worse.”
Professor Greste said the rapid decline of Afghan media in the past few weeks was tragic.
“Over the last 20 years it's flourished in ways that I think few people really could have imagined, we've seen an incredible array of newspapers and television networks and radio stations and websites and so on - all springing up doing some amazing work,” Mr Greste said.
“To see all of that unravel now I think is desperately sad and tragic for the country.”
Professor Greste, the UNESCO Chair in Journalism and Communication, said he was yet to hear from the government after writing to it to advocate for media workers in Afghanistan weeks ago.
In a statement, the Department of Home Affairs said it did not comment on individual cases and it could not provide detailed information as it was prioritising the welfare, privacy, safety and security of those seeking evacuation from Afghanistan.
"The government is working to ensure that visa options continue to be available to Afghan nationals, both within Afghanistan and those displaced from their home country, through Australia’s long-standing Humanitarian and Migration Programs," a spokesperson said.
"Those who have been granted visas and are still in Afghanistan will be contacted over the coming weeks by the Department of Home Affairs about what to do when it is safe."