Voodoo0Child,
As a mother I have to say that it is probably better to be honest. Your mother's wish for you is probably that you not get pregnant and not get infected by an STD. There might be some screaming and shouting, but that is the pains a mother goes through when her daughter grows up. I am sure she wants only the best for you, even though it may not seem so to you now.
So my advice will be to sit her down and go: "Mom, the other day when you asked me is I had sex before you scared me and I lied and now I feel bad about it. I am growing up and I am starting to think about sex and I want to be responsible and careful about it. I know you want only the best for me so please help me to be safe and protect myself from pregnancy and infections."
If you do not feel comfortable doing it in person, write her a note.
One thing I am sure about is that it is a much easier thing to do than tell her that you are pregnant or have an STD.
And please do not have sex again until you understand how to protect your own health.
Take care