To solve this issue please follow the below steps:
Please note It seems that the version of SQL 2012 that comes within the installation and configuration of AADConnect does not support TLS.
This is incredibly important, for, as you may know, AADConnect needs and uses TLS 1.2.
a. Manually uninstall AADConnect and remove all components in relation to AADConnect.
b. Re-install AADConnect with the same original download link: https://www.microsoft.com/en-us/download/details.aspx?id=47594
c. Once the configuration wizard can be found on the machine, do run it, however, do not click on Configure. Simply close it.
This will allow AADConnect to automatically confirm the License Agreements.
d. Once those steps are done, please install the latest version of Microsoft SQL Server 2012 Native Client, the download link can be found here:
https://www.microsoft.com/en-us/download/details.aspx?id=50402
c. Then, once you have successfully installed Microsoft SQL Server 2012 Native Client, you may go ahead and run Azure AD Connect and go through the Custom Installation option.
From the research I did, I found out that, Azure AD Connect comes with a version of the Microsoft SQL Server 2012 Native Client that does not support TLS. This issue does not always affect everyone, however, when it does, this is resolved by installing the SQL Server independently as a stand-alone download.