More than 80 remaining Taliban prisoners holed up in a prison fortress were flushed out from their hiding places.
Northern Alliance soldiers sprayed water into their basement hiding place in the prison near Mazar-e-Sharif.
Three came out first and offered to surrender, and then the other 82 emerged.
"The soldiers poured water into the basement and it was very cold so they all came out," Dr Arif Salimi, head of the local health office in Mazar-e-Sharif. "They couldn't take it any longer."
Many of the prisoners were injured, Mr Salimi said, without providing any further details. Some are being treated in hospitals and others were imprisoned again.
In Geneva, a spokesman for the International Committee of the Red Cross, said the ICRC has begun registering some of the Taliban prisoners.
"Registering for us is a key thing," Kim Gordon-Bates said. "Once a person exists, they can't disappear."
General Rashid Dostum, the Afghan warlord whose headquarters are in the Qalai Janghi fortress, had said that there could be a few remaining prisoners hiding in the southern section of the compound.
Local health workers had already begun collecting the dozens of bodies of those killed in the three days of fierce fighting that began November 25 in what officials described as a prison revolt.
But on Thursday, at least two health workers were injured with gunshot wounds when attempting to retrieve bodies from the prison basement.