In SharePoint online, unique permission 5000 limit is not per site or site collection, it is per list or library
Microsoft recommends to have 5000 unique permissions but it can be increased to 50,000 - we should not increase the limit until we actually need it. For large lists, design to have as few unique permissions as possible. we need to design such a way so that we can keep unique permission below 5000.
Statement from Microsoft for unique permissions in list or libray level:
"
Unique security scopes per list or library - The supported limit is 50,000, but the recommended general limit is 5,000. Above 5,000, access control list (ACL) size starts to matter. Although you can add scopes up to the supported limit of 50,000, Microsoft doesn’t recommend it unless you have a very specific scenario in mind. For large lists, design to have as few unique permissions as possible."
Please refer the below document for the limits in SharePoint online:
SharePoint Online limits
How to increase the limit to 50000?
From your office 365 help desk support, raise a ticket to Microsoft referring the above Microsoft document, they will guide you how to do that... their customer support is very good, within a few minutes after raising the ticket you will get a call from them.