The judge accepted the request and put off the case for a fortnight during proceedings held behind closed doors in Rawalpindi, sources informed.
It could not immediately be ascertained whether the FIA will appoint a new chief prosecutor in place of Ali or the case will be taken over by his deputy Chaudhry Azhar.
Ali was killed by unidentified gunmen near his home in Islamabad in an execution-style drive-by shooting on Friday.
No group claimed responsibility for the attack.
Besides the Mumbai attacks case, Ali was also handling the Benazir Bhutto assassination case, over which former president Pervez Musharraf was recently arrested by the FIA.
The seven Pakistani suspects, including Lashkar-e-Taiba commander Zakiur Rehman Lakhvi, have been charged with planning, financing and executing the attacks that killed 166 people in Mumbai in November 2008.