Azhar Ali will remain Pakistan's one-day captain after his offer to resign over Mohammad Amir's presence at a Lahore training camp was rejected.
Azhar and former captain Mohammad Hafeez had initially refused to join the camp before opting to return.
The Pakistan Cricket Board (PCB) says Azhar "will continue as captain".
The PCB statement added: "Azhar Ali met the PCB chairman [Shaharyar Khan]. He tendered his resignation. The chairman didn't accept his resignation. Azhar Ali agreed."
Hafeez said last month that he could not "share the dressing room with someone who hurt my country's integrity".
Meanwhile, a Pakistani court has rejected a petition against the inclusion of Amir in the national team with the 23-year-old set to be included in the squad for next month's limited-overs tour of New Zealand.
In 2010, aged 18, Amir pleaded guilty to bowling no-balls at pre-arranged times during Pakistan's fourth Test against England at Lord's.
He served half of a six-month jail term, while team-mates Mohammad Asif and captain Salman Butt served six and seven months respectively.
Former Pakistan captain Imran Khan has backed Amir's return to international cricket but Test skipper Misbah-ul-Haq has said he feared the bowler's comeback would prove a big distraction for the team.