Younis was appointed last week to fill in for Inzamam-ul-Haq after Pakistan's regular captain was banned for four matches by the International Cricket Council following the Oval Test fiasco in August.
The PCB said that Yousuf, 32, is now captain for the upcoming trophy and all-rounder Abdul Razzaq is vice-captain.
It did not say whether Younis would still play.
The PCB held a day of frenzied meetings after Younis made his surprise resignation at a press conference in Lahore earlier Friday, just two days before the team were due to fly to India for the Trophy.
Younis said earlier he did not want to be a "dummy" captain.
The 32-year-old Yousuf, who has played 70 Tests and 223 one-day internationals, has led Pakistan in four one-day internationals, losing two and winning two. In his three Tests as captain Pakistan lost two and won one.