Yes. The Japan Consulate in San Francisco will consider an application if the USA Immigration status is expired, as long as you submit the original and a copy of your I 797 approval.
You should also submit the original and copy of the expired USA visa. In the case of an expired F1 visa, the applicant should also provide the original and a copy of their most recent I 20. If you have held an EAD card, you must also provide the original and a copy also