In order to remove the org administrator you will need to add another org admin and then you can remove the user who left. Since you are only a site admin, you will need to use the users account who left.
You can take a look at the below article as well. It tells you how to remove an org admin. It does not specify you need at least one but that is the case.
If you can under users, you should be able to access his account and reset his password. Then you can log in and add a new org admin. If that does not work, you would need to contact Atlassian for support. You should be able to reset his password though and then sign in.
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