The stuff within the parens is a capture - if you move the § outside of the capturing parenthesis, and then add your required entity to the replacement text, it should do what you need.

So, if you have a replacement s/(A\S+)/[$1]/ and want to replace A with something else, you would use s/A(\S+)/[B$1]/ instead, replacing A and B as necessary.

A read of perlre, perlrequick, and perlretut may be helpful. I also wonder if HTML::Entities may be a more appropriate solution to the second requirement.