A Pakistan Cricket Board (PCB) statement said Zulqarnain breached the terms of his contract.
"PCB has suspended the stipend contract of Haider for violating terms and conditions and a three-man committee will look into the facts surrounding the incident regarding his disappearance," it said.
The 24-year-old fled the team hotel on Monday without informing the team management. He later told Geo News that he received death threats in Dubai after helping Pakistan win the fourth one-day international against South Africa.
He made 19 not out to help Pakistan turn the tables and win the match by one wicket in Dubai on Friday.
Zulqarnain did not turn up for the final match on Monday, which South Africa won by 57 runs to take the five-match series 3-2.
Team manager Intikhab Alam, team security manager Khawaja Najam and PCB official Subhan Ahmed are the members of the fact-finding committee, the release said.
"PCB is trying to get in touch with Haider but the attempts to contact him have so far remained unsuccessful. No further comments on this matter will be made till further information is available with PCB," it added.
Intikhab denied the team management was responsible for Zulqarnain's case, saying they had no prior information about his fleeing from the team hotel.
Zulqarnain has reportedly sought political asylum in Britain and announced his retirement from international cricket.
