Radovan Krejcir was arrested on Friday at his home in Johannesburg on a charge of kidnap and assault.
His lawyers filed a court application, saying he needed medical attention and risked kidney failure.
Krejcir has repeatedly denied having links to the criminal underworld.
The police have been accused of reacting slowly to reports of his alleged involvement in the killing of underworld bosses, reports the BBC's Pumza Fihlani from Johannesburg.
A number of his associates have been killed in separate incidents in recent months, local media report.
In July, Krejcir survived an attempt to kill him carried out by guns hidden behind a car number plate operated by remote control opened fire on him in Bedfordview, a suburb east of Johannesburg.
Krejcir reportedly described the shooting as "something out of a James Bond film".
He is challenging the government's attempts to extradite him to the Czech Republic, where he was convicted in absentia last year on tax fraud charges.
He moved to South Africa in 2007.
Our correspondent says South Africans have been keenly watching Krejcir's extraordinary career over recent months and the series of gangland shootings and killings with which he is allegedly linked.
They are worried that it might show that a well-connected, sophisticated and violent underworld still exists on the streets of Johannesburg, she says.
On Saturday, police chief Riah Phiyega said Krejcir's arrest was a major breakthrough.
"There are many investigations that are taking place, even on the charges that the suspects have been arrested for. We hope to arrest more suspects as the investigations unfold," she told reporters in the capital, Pretoria.
She did not reveal details of the charges against him.
The police watchdog, the Independent Police Investigative Directorate (Ipid), said it had launched an investigation into Krejcir's claim that he had he had been tortured.
Police are accused of taking him to an open field where he was "allegedly shocked with a taser and a plastic bag was placed over his head to suffocate him", Ipid said in a statement.
The High Court in Johannesburg ordered that Krejcir be transferred to hospital after his doctor testified that his injuries were consistent with those of someone who had been assaulted.
He could face renal failure if he was not taken to hospital, the doctor said.
In his ruling, Judge Ramarumo Monama said the doctor was a credible witness.
"He has provided more than enough evidence," local media quotes the judge as saying.
A South African court has ordered that a Czech businessman accused of links to organised crime be moved from prison to hospital after claims he had been tortured by police with a taser gun.