Al-Zery, together with Ahmed Hussein Agiza, another Egyptian asylum seeker, were expelled from Sweden after being identified as possible supporters of al-Qaeda.
The pair were then handed over to US agents, put on a plane leased by the Pentagon and flown to Egypt, according to Saepo, the Swedish intelligence agency.
The two men claimed they were mistreated by the US agents during their transfer to Cairo, and then tortured during their detention in Egypt.
In Egypt, Agiza was handed a 25-year prison sentence for terrorism which was later shortened to 15 years. Al-Zery was freed by an Egyptian military court though he remains under supervision.
Sweden has not dealt with the case of Agiza, who remains in prison in Egypt, because he had not made any request to the government, a spokesman for the Migration Ministry said.
Al-Zery has applied for Swedish citizenship.
Sweden's ministry of justice said in a statement on Thursday that "the guarantees given by the Egyptian government ahead of the [expulsion] decision on Dec. 18, 2001, should not have been considered sufficient".
"In light of the former government's wrongful measures, which I and many others have criticised, I am very happy with this decision," Tobias Billstrom, the migration minister, said.
Egypt has denied mistreating the two men.
Council of Europe investigator Dick Marty last year cited Al-Zery and Agiza among the cases he used to back his conclusion that 14 European countries had colluded in a "global spider's web" of transfers of terrorist suspects and secret CIA prisons.