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Younis, 37, made the shock announcement on the morning of the first ODI against England at Abu Dhabi, having previously been outspoken in his criticism of the selectors for dropping him in the wake of Pakistan's World Cup exit in March.
He was dismissed for 9 in his 265th and final appearance during Pakistan's run-chase at the Sheikh Zayed Stadium, bringing to an end a 15-year career in the format that had begun against Sri Lanka at Karachi in March 2000.
However, Shaharyar was unimpressed by Younis's actions. "I am disappointed at not only his decision to retire from ODIs but also the timing of his decision," he was quoted as saying by PTI.
"Younis has been doing well and that is why the selectors felt he should be played again in the one-day matches. For me it is surprising he announced his retirement today."
Shaharyar did, however, confirm that the PCB would arrange a suitable send-off for a man who has scored 7249 runs in the format at 31.24, with seven centuries, albeit just the one since 2008.
Haroon Rashid, Pakistan's chief selector, also expressed his confusion at Younis's actions.
"When I went to Sharjah to meet with the team management and I also talked to Younis, he gave me no indication he was planning to retire from ODIs after the first match of the series," Haroon said.
"We picked him keeping in mind that we needed an experienced batsman in the middle order to stabilise the batting. We picked him keeping in mind our future assignments. He never discussed this retirement thing with us."
"The team will remain balanced but at no stage did Younis convey any desire to us he wanted to retire," he added.
Mohsin Khan, the former coach, speculated that Waqar Younis's reluctance to have Younis back in the one-day squad may have played its part.
"It makes no sense that after being picked for the full series in the one-day squad after such a big gap he should decide to retire after playing the first match. Definitely I think something has happened in the last 48 or 24 hours to have upset Younis who is very sensitive and a self-respecting individual," Mohsin told Geo Super channel.
"I think the job of the captain, manager and coach is to not only motivate the players but also make them feel comfortable and wanted. I think in Younis's case this didn't happen and no one tried to speak to him to find out his feelings."