This should be doable, although not by simply uploading a .CSV file and downloading the output. The easiest way would be to use some of the PKI Client Cmdlets in Windows PowerShell. These are PowerShell commands that let you interact with a Microsoft CA from a script or the command line.
The first step, would be to generate a certificate request using the DN information you find in the .CSV file. A great tutorial on generating the CSR can be found here. Once the certificates have been approved on the CA, you can export them using the relevant PKI Client Cmdlet, Export-PfxCertificate
via your PowerShell script.
Hope this helps!