Mouse across the list of purchases to the app you want to remove from that list. Click the X that appears next to the app status. Should be on the far right.
If you have actually deleted the app by trashing it, and it's an app that you purchased, then it should show up in purchased apps list, with an Install button. The delete X should appear to the left of that button when you mouse down to that app in the list.
You can remove any Purchased app from that list - or all of your apps,
BTW, the App Store will NOT actually remove an app if it is still actually installed. All you can do on that window is delete the item in the Purchased list. It will no longer appear, until you View your Account, and click the Reset Purchases (or whatever that button says)
BTW, the proper method to uninstall a purchased from your Mac, is to use the Launchpad. Click and hold your app in Launchpad, until it shakes - then click the X near that app icon. The app will then be correctly removed (uninstalled).
So, the sequence is: Remove using Launchpad. Then, remove the app entry in the App Store Purchased items list.