As has been said previously, you obviously have done something right because she is talking to you, but I totally understand your concerns because she is very young. 13 is way too young to be involved in a sexual relationship, but obviously it happens sometimes.
There are 2 issues that need addressed, her health (she most definitely needs to be taking precautions regarding STDs and pregnancy) and her emotional relationship with this boy.
How long have they been together? What made her decide that the time was right to do this? You really need to explore (you can fall apart later, in private) her reasons for doing this. Is she going to do this with every boyfriend that she has because she thinks she's supposed to?
These are definitely questions that need asked. I hate to bring this up, because you definitely could not have just predicted this, but how much unsupervised time does she have to spend with him? It sounds like the reins need pulled in a bit because she is moving really fast for her maturity level, 13 is very, very young. I say this because even with BC, a 13 year old is rarely mature enough to be responsible about it ALL of the time (hell, even a 25yo can be irresponsible about using precautions)...but 13...that's way young. I am not suggesting punishment or grounding, just less unsupervised time.
Also, I am assuming this was totally consentual because of the tone of your OP, but was this a situation that was a heat-of-the-moment type thing or one that they had been planning?
As mentioned before, TALK often and openly, find out where she is at and why. big hugs, it is not easy parenting teens....sounds like you are really open with eachother, that is 1/2 the battle.