No, you can't file the business separately unless it is set up as a corporation or partnership. Even then, it would produce a K-1 that you have to report on your personal taxes.
A sole proprietor small business has to be included on a Schedule C with your married filing jointly return.
You will need to amend the return you filed. Here is a link to amendment instructions.
https://ttlc.intuit.com/replies/3288565
