How do you politely tell your friend that he/she is not invited in your wedding when they ask?

If you're not accommodating this friend of yours, then it means that they are simply not close enough to you. And since a wedding is a major development in your life, they would naturally understand your predicament. The best way is to be honest and tell them that you are having a low-key wedding and have invited only close friends and family. Nobody will fight with you about not being invited if you're honest.