I’m not sure there is anything that can be done actually. The code for the single post and pagination is just the_content immediately followed by the pagination. So since the ad is getting added after the_content I’m not sure there is anything we can do to interact with it.
You could try adding some css to highlight the pagination a bit more. Try adding the following CSS to your Quick CSS (located under the Styling Tab in the theme options) or the custom.css file in the css folder of your theme files::