You'll need to recompile the application against .NET 3.5; install a hotfix on the machines that run it; and change the code to enable TLS support:
Support for TLS System Default Versions included in the .NET Framework 3.5 on Windows Server 2012[
^]
Alternatively, you can upgrade your application to .NET 4.5 or higher. You will still need to either change the code to enable TLS 1.2, or set a flag in the registry on all machines where you application runs:
Enable strong cryptography in .NET Framework 4.5 or higher[
^]
NB: if your application is running on Vista, Server 2008, or any earlier version of Windows, you
cannot support TLS 1.2 even if you install the hotfix.