You say you're sure, but you can't ever really be. It's easy enough to spill or sit on something. And it doesn't even matter: you don't need to tell her what kind of stain it is, just that it's there.
So just keep it simple, like you presumably would if it were anything else: "hey, I think you have something on your pants."
She can figure it out and take care of it from there, whatever it is. If that is what it was, she gets to save face and hope that you didn't realize. If it's not, then you've avoided making an embarrassing mistake. Either way, neither of you have to have a presumably awkward conversation about menstruation.
Be sure to say this in a way that no one else will overhear, and ideally not face-to-face either, to minimize embarrassment and remove any need to actually talk about it further. An IM would be a good choice assuming IMing is normal in your office and you can do it immediately: it doesn't put either of you on the spot, she can take a second to answer, and she doesn't have to be in front of a person when she's in an embarrassing situation. If you're really graceful and able to project a no big deal vibe, you could try in person, but given that you were already uncomfortable and likely to be awkward and she was on her way out so you'd have had to chase her, it seems like a more difficult option. (If IMing each other isn't normal in your office, or you can't count on her getting it right away, then yes, do it in person as discreetly and casually as possible.)