The Pakistan Cricket Board had installed fellow batsman Mohammad Yousuf as captain after Younis declined the role first bestowed upon him stating that he didn't want to be a "dummy captain".
Naseem Ashraf, the new PCB Chairman after taking over from Shaharyar Khan this week, said that Younis had agreed to captain the side again and Yousuf would return to the role of vice-captain.
"Younis has agreed to lead the side again after I spoke to him and explained things to him," Ashraf said.
Former PCB Chairman Khan resigned on Friday citing the fourth Test debacle at the Oval and Younis' resignation as reasons for his decision.
28-year-old Younis said he had been under great mental strain over the past few days and that his respect for Ashraf had swayed him to take back the captaincy.
"I know the last two days have also been hard on the people who wanted to know why I had left the captaincy," Younis said.
"I just hope we can now put everything behind us and try to do well in the tournament."
Ashraf also announced that former leg-spinner Mushtaq Ahmed would not be attending the biennial one-day tournament in the position of assistant coach.
"We felt there is no need for an assistant coach with the team at this stage so Mushtaq has been released," Ashraf told Reuters.
The appointment of Mushtaq as assistant coach has been criticised, as he was barred from holding any post with the team after a match-fixing inquiry was conducted by Justice Malik Mohammad Qayyum in 1998.
Pakistan's regular skipper Inzamam-ul-Haq is serving a ban of four one-day international matches for bringing the game into disrepute during the fourth Test against England at the Oval in August.