If he's still in pain this morning, I'd definitely take him back to the vet. Even if he's not having a serious reaction, the vet can give him a shot of dexamethasone, which will make him more comfortable. I'm sorry I didn't see your message sooner!
In the future, you may want to rethink your vaccination strategy. First of all, I don't know what area of the US you're in, but my vet does not give the Lepto vaccine because it's not a problem here in Indiana, and Lepto is one of the most common vaccines to cause reactions. Secondly, for toy breeds my vet *always* splits the vaccines into at least two, preferably three trips instead of giving a big combo vaccine. He says (and I agree) it's just too hard on a tiny dog's body. Also, after the initial puppy vaccines, my vet now recommends titers for chihuahuas instead of vaccines, so that's something you may want to consider next year. Anne
