Look at the documentation of certutil.exe and -addstore option.
I tried
certutil -addstore "Root" "c:\cacert.cer"
and it worked well (meaning The certificate landed in Trusted Root of LocalMachine store).
EDIT:
If there are multiple certificates in a pfx file (key + corresponding certificate and a CA certificate) then this command worked well for me:
certutil -importpfx c:\somepfx.pfx
EDIT2:
To import CA certificate to Intermediate Certification Authorities store run following command
certutil -addstore "CA" "c:\intermediate_cacert.cer"