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Younis tendered his resignation on Tuesday at a meeting of the parliamentary sport's committee, which summoned him to explain why Pakistan lost to Australia and New Zealand in the September-October Trophy in South Africa.
"These last few days were torturous and the allegations hurt me no end," Younus told AFP.
"Ever since we returned from South Africa, I was hiding from people as if I have committed a crime. It was painful because I played my cricket for pride, for my country and not for money."
Pakistan's narrow defeat against Australia in a group match and upset loss to New Zealand in the semi-final sparked allegations that the team had thrown the matches, in part to knock arch-rival India out of the tournament.
Legislator Jamshed Dasti, chairperson of the sports committee, summoned Younis, coach Intikhab Alam and Pakistan Cricket Board (PCB) chairperson Ijaz Butt to explain, with Tuesday's meeting clearing Pakistan's team of any wrongdoing.
Younis, 31, said he was shocked by the initial match-fixing allegations.
"It was the limit and being an honourable Pathan (Pashtun), I felt I must resign. It's not an emotional decision. I am badly hurt," he said.
Younis's initial resignation was rejected by Butt, who told AFP on Wednesday that he would consider the matter further.
"He (Younis) was naturally hurt over the whole affair and I can realise that. The allegations were serious and without evidence they are damaging. I will discuss the matter with him soon," Butt said.
Younis said it was up to the PCB to take a decision on his resignation.
"Ever since I have taken over as captain I have sacrificed a lot. I took the team with me, the management with me, but this is the limit and now it's up to the Board to decide on my resignation," said Younus.
Younis replaced Shoaib Malik after Pakistan's upset 2-1 defeat against Sri Lanka at home in January.
Although Pakistan lost a one-day series against Australia in United Arab Emirates in April-May, a month later they went on to win the World Twenty20 in England -- a victory which sent the cricket-mad nation into a frenzy.
Pakistan then lost a Test and one-day series in Sri Lanka despite playing well in July-August.
It was on the Sri Lanka tour that the first match-fixing allegations surfaced, after the Pakistan team management revealed some bookies tried to make contact with Pakistani players, but were turned down.
Pakistan's defeats from winning positions in the first two Tests prompted former players to call for an inquiry, but the International Cricket Council cleared the team of any wrongdoing.