I am aware of using .gitignore file to exclude some files being added, but I have several config.php files in source tree and I need to exclude only one, located in the root while other keep under revision control.

What I should write into .gitignore to make this happen?

From the documentation:

If the pattern does not contain a slash /, git treats it as a shell glob pattern and checks for a match against the pathname relative to the location of the .gitignore file (relative to the toplevel of the work tree if not from a .gitignore file).

A leading slash matches the beginning of the pathname. For example, "/*.c" matches "cat-file.c" but not "mozilla-sha1/sha1.c".

So you should add the following line to your root .gitignore:

/config.php