The Court of Arbitration for Sport (CAS) in Lausanne will now hear the case.
WADA spokesman Frederic Donze said the action was being taken "in the interest of doping-free sport" and the "uniform application" of its code in all disciplines.
Pakistan Cricket Board (PCB) chairman Dr Naseem Ashraf has insisted, however, that the matter is now closed once for all and it doesnt fall under the perview of WADA.
Shoaib was originally banned for two years and his younger team-mate for a year after traces of a banned steroid, nandrolone, were found in their samples, but a three-man panel subsequently upheld their appeals by a 2-1 majority.
The two players claimed the drug was present in supplements they had taken, but they had not taken it knowingly.
The International Cricket Council is, however, a signatory to WADA's anti-doping code and the agency believes Pakistan, as one of the ICC's full members, should therefore be subject to its provisions.
"WADA has exercised its independent right to appeal, provided in the World Anti-Doping Code, to the CAS against the PCB's appeal panel decision to overturn the sports sanctions of two athletes who recently tested positive for performance enhancing drugs," said Donze.
Since the lifting of the ban, Shoaib and Asif have been named in Pakistan's preliminary squad for a tour to South Africa and they are both hoping to play in the World Cup in the West Indies which follows.