Pakistani security sources confirmed that Memon was handed over to the US.
Human rights groups have raised suspicions that Memon and several others were held by a secretive Pakistani intelligence agency probing the January 2002 kidnapping and beheading of Pearl.
When Memon reappeared, his brother said he was in extremely bad health, severely malnourished and barely able to talk.
This month, Memon, 44, was brought to the Supreme Court in Islamabad on a stretcher.
The court, which was handling cases of missing people, was alarmed at his condition and ordered that medical treatment be provided at the government's expense.
However, Memon, a father of five, died at Liaquat National Hospital in Karachi on Friday, his brother said. More than 300 people attended his funeral.
Ali Azmat Abidi, doctor at Liaquat hospital, said Memon died from tuberculosis and meningitis.
Pearl was kidnapped in Karachi in January 2002 while researching a story on Islamic extremists. A video of his decapitation was later delivered to the US consulate.
Memon was wanted for questioning by the police but he could not be found and was declared a fugitive.
Sheikh Omar, a British-born Islamist and three Pakistani Islamists were sentenced to death in 2002 for Pearl's murder, but have appealed against the verdict.
Pervez Musharraf, the Pakistani president, has been criticised by international and domestic rights groups for detaining people illegally in the name of the fight against terrorism.