In the absence of anything relating to the quality of the work or something that was done incorrectly, I would say no. If he didn't obtain a quote from you before you commenced work then one might assume he was prepared to pay standard industry rates (which I assume your invoice reflects).
Thing is, if you don't he probably won't pay you anything and I doubt the amount of money he is docking is sufficient to justify pursuing legal action to recover it. Also, you may not get anymore work with this guy in the future. I don't know whether that's what you want though in any event.
If he was to remove the glass and tell you to take it back, this would not absolve him of the obligation to pay you. You have been contracted for services, which you performed and you are entitled to be paid.