It is not possible to use an ASPX+Portal page to my knowledge with a portal master template.
The 'benefit' of an ASPX portion is that you can define your various page methods (such as the Page_Load, OnInit, etc). However this is completely unnecessary as you can do the same in a purely Portal page template.
There are 2 ways to do this:
1: In the "Layout" of the Portal Page Template, you can insert a script tag and put in your content as you normally would. Just make sure the Layout type is "ASCX"
Your page template content here
protected override void OnInit(EventArgs e)
// Your own custom logic here
2: Create a custom control (ASCX) that contains your logic / output, and either turn it into a webpart or use the "Custom Control" web part and point to the file.
With these two things, you can do anything you could do with an ASPX or ASPX+Portal page without the actual ASPX.