It wouldn't be a wart - it's far too soon to see that, as the incubation period (the point from infection to when you see symptoms) for that is at least a few months.
It is possible to get herpes while wearing a condom, and the timing fits, but the symptoms really don't. Usually, you get symptoms at the point of infection, and since you wore a condom, you'd expect that your symptoms would be outside of the condom-protected area. That's not a hard and fast rule, though. One single pin-prick sized spot isn't typical of herpes, either - it's usually a cluster of blisters, or something that looks like a paper cut.
The blisters usually take a few days to break and then scab over. It sounds like it scabbed over in a day? Am I understanding that correctly?
So what is it? That's hard to say, as it could be lots of things. It could be just irritation - did it rub against a zipper? It could be a fungal infection, or the start of one. It could be dermatitis, an allergic reaction to something. The only way you'll know is to get it checked.
I wish I had more definitive answers for you, but let us know what the doctor says.