You cannot for visa directly through the Japanese embassy. The embassy only issues official and diplomatic visas. This means you should apply for visa by visiting visa application center like VFS.
If you are applying through VFS global, you need to book for your visa submission. The visa appointment can be booked on the VFS website.
You will be informed of the precise time and date for application submission. You will get an email confirming your appointment, which you should print off and bring with you to your visa appointment.
Ensure that you follow the steps mentioned the website of VFS to start your application process. You will get a proper guidance on how to submit your documents.