American in Japan/online ticket

Dear Sir or Madam,
I am a longterm (permanent residency) resident of Japan, but am an American citizen. I would like to corss the border into mainland China from Hong Kong for but a few hours or so while on a trip to Hong Kong in December.
I have purchased my ticket to Hong Kong (with an in-transit stop in Shanghai) online and am not using a travel agency.
Can I apply for a visa at the embassy? If not, what travel agency would work with me if I am not purchasing a ticket from them?
Thank you very much.