Hello @lior zivi · Welcome to QnA platform and thanks for your query.
Any Azure AD Registered application can be added to Conditional access, it is not required to be gallery application. You should be able to search the application by using application name or application id, under cloud applications blade of conditional access policy.
However, if you are unable to search the application in CA Policy, make sure WindowsAzureActiveDirectoryIntegratedApp tag is added to the application. You can use below PowerShell Cmdlet to add this tag:
Set-AzureADServicePrincipal -AccountEnabled $true -AppId your_app_id -AppRoleAssignmentRequired $true -DisplayName your_app_name -Tags {WindowsAzureActiveDirectoryIntegratedApp}
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