The Court of Arbitration for Sport (CAS) said on Monday it was forced to dismiss WADA's appeal since the Pakistan Cricket Board (PCB) does not recognise the court in its regulations.
Strike bowlers Shoaib and Asif were handed two and one-year bans in November by the PCB's Anti-Doping Commission after testing positive for the banned steroid nandrolone.
The punishment was controversially lifted one month later by the board's Anti-Doping Appeals Committee, which said the pair had successfully argued they had taken supplements in the belief they did not contain prohibited substances. WADA's strict liability rules hold athletes responsible for any substances found in their bodies.
"Following this case, we have amended the ICC Anti-Doping Code to ensure we have more powers to intervene if we feel a member is not doing all it can in the fight against drugs in cricket," ICC acting CEO Faisal Hasnain said in a statement.
"In line with the amendments, the ICC now has a right of appeal if a member that is not WADA-compliant makes a decision which is inconsistent with the WADA code.
"Furthermore, while such an appeal is pending, the relevant players can be target tested by the ICC up to 60 days before one of our events."
The CAS said it made its decision "with some considerable regret" because its rules required that a direct reference to the CAS be contained in the regulations of the body whose decision was being appealed.
WADA said in a statement on Tuesday it was satisfied the court had termed the exoneration as an 'unsatisfactory' decision and urged the ICC, which adopted the WADA Code in July 2006, to take steps to implement the code in all aspects.