Here's how to to do it properly.
1. Open POL.
2. Click on "The Elder Scrolls 4 - Oblivion" and then "Configure" in the right hand pane.
3. In the dialog that opens click on the "Miscellaneous" tab and then the "Run a .exe file in this virtual drive".
4. A file selection dialog will open. On the left hand side click on your user directory and then double click on "PlayOnLinux's virtual drives" in the main pane. This is assuming you placed the patch file in the game directory inside the Oblivion wine prefix like I did.
5. Keep drilling down to the location of the patch file, select it and click on "Open".
The patch should apply properly this way.
GL!