You can do this by using the OnShow and OnHide events for your pop-up widget (assuming it is a widget, group of widgets or dynamic panel and not a separate pop-up browser window.)
Look in the "More Events" list under the Interactions in the Properties panel and you'll see OnShow and OnHide. Select OnShow and in the Case Editor dialog, select Disable, then select your "background section" (one or more widgets.) Do the same for OnHide except Enable those same widgets.
Or, if you want the entire page to be effectively disabled while the pop-up is shown, you can choose "More Options : treat as lightbox" under the Show event (in the Case Editor dialog.) This will put a semi-opaque mask over the entire page, underneath the pop-up widget. Clicking anywhere on that mask will close the pop-up but will not trigger any other interactions.