I don't think this is possible. You should convert the .pfx certificate to .p12 before. I am sure this is possible on both the Mac OS X and Windows operating systems. For the first one, I remember the procedure without having the need to startup my computer: import the .pfx certificate on Keychain Access and then export it in the .p12 format.
I haven't tried this, but you may be able to do this if you manually sign rather than use Extension Builder's export wizard. You can find some information about how to manually sign in the packaging and signing toolkit, available here: http://www.adobe.com/devnet/creativesuite/sdk/eula_cs5_toolkit.html