The July verdict meant that emails held on a server in Ireland, that the US government was seeking to obtain saying they had relevance to a drug-trafficking operation, were out of the government's reach.
The DoJ has now filed for an appeal to be heard by the full appeals court of the Southern District of New York, claiming that the previous ruling will get in the way of investigations.
The Second Circuit Court of Appeals based in New York reversed that decision.
The original warrant demanded that Microsoft release the contents of all emails stored in the particular account; records and information about account identification (including username and method of payment); all user records, including images and files; and all communications between Microsoft and the user about the account.
American companies have lost business due to fears that any data held within US jurisdiction will be within grasp of the NSA after the Snowden revelations.
Firms have thus resorted to provide data repositories outside the US. Microsoft set up cloud services in a German data centre in March to avoid being subject to US laws.