Right, the commands are sftp and ssh
Your question is a bit like asking for a Windows version of WINE, or a Linux version of Cygwin. sftp, scp, and ssh are native programs in Linux. They were born in Unix/Linux. WinSCP and Putty are GUI tools that allow you to access those protocols from a Windows environment.
I think you're just thinking about things backwards. You aren't looking for Linux replacements for WinSCP and Putty, you're looking for the originals that WinSCP and Putty are based on.
Just open a terminal, and run "sftp", "scp", or "ssh". You can use the man pages to see how to use them, but it should be pretty straight forward:
scp user@host:/path/to/remotefile localfile
scp localfile user@host:/path/to/remotefile