More than 17,700 people are estimated to have died in custody in Syria since the country's conflict began in March 2011, an average of more than 300 each month, the watchdog said in a report.
Anyone seen as an opponent of the government is at risk of arbitrary detention, torture, enforced disappearance and death in custody, according to Amnesty.
It said the report was based on interviews with 65 torture survivors, mostly civilians, who described "appalling abuse and inhuman conditions" in intelligence agency detention centres and the Saydnaya Military Prison near Damascus.
Most described witnessing at least one, if not several, deaths in custody, Amnesty said.
Detainees are frequently subjected to a beating, known as a "welcome party", after their arrival at a prison by guards using tools such as silicone bars or hoses.
"They had to break us; they treated us like animals. They wanted people to be as inhuman as possible," according to a former detainee identified as Samer, who Amnesty said was arrested while transporting humanitarian supplies.
"I didn't see anyone die but I saw the blood, it was like a river," he said.
- 'Getting rid of the weak' -
Omar S, who was a 17-year-old high-school student at the time of his arrest in 2012 after taking part in demonstrations, said the detainees were asked upon their arrival if they were ill.
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"It felt like the purpose was death, some form of natural selection -- to get rid of the weak as soon as they arrive," he said.
"They first asked my friend and he said, 'Yes, I have breathing problems -- I have asthma.' They started beating him until he died, right there in front of me."
The rights group said it had documented cases of rape and sexual violence against both men and women.
They include Said, a pro-democracy activist, who said that he was suspended by one hand while blindfolded.
"While I was hanging ... they used an electroshock baton to hit my penis. Then they took the electroshock device and inserted it into my anus and switched it on. This was my first experience of rape. Then one of the guards asked for my face to be uncovered and I saw my father there. He had witnessed all of it."
Access to food, water and sanitation facilities is often severely restricted in regime prisons and infestations of scabies and lice thrive along with diseases, according to the report.
Amnesty urged world powers, in particular Russia and the United States, to pressure the Syrian authorities and armed groups to end the use of torture and other ill-treatment.
"For decades, Syrian government forces have used torture as a means to crush their opponents," said Amnesty's Middle East and North Africa director Philip Luther.
"Today, it is being carried out as part of a systematic and widespread attack directed against anyone suspected of opposing the government in the civilian population and amounts to crimes against humanity. Those responsible for these heinous crimes must be brought to justice."