Quite a few queries online about this.
Refers to a Mac.
Assumes iTunes is open and your iPhone is plugged into your computer.
I must just have a quick rant: I HATE the way that "synch" works - one cannot tell which set of data are being synched to what, which data are being synched ... I could go on ... clearly Steve never had much to do with the software aspects of his desirable kit.
Anyway, look at the top of the iTunes menu under Library and you'll see Apps. Click that and you have 2 views of your apps, either Apps (all of them) or Genres (inconvenient in my opinion).
Left click on an app and one option is Delete. Also you can Show in finder, and I suppose delete it from the list of files as well.
You also need to delete it from the iPhone or else it will simply copy it back to your computer next time you "synch". To do this, hold your finger on the app on the iPhone screen and then press the little cross in the corner of the icon.