• $_ = reverse(join(',', reverse($_) =~ /.{1,3}/g));
  [download]

  or

  $_ = join(',', split(/(?<=.)(?=(?:.{3})+\z)/, $_));
  [download]

  or

  $_ =~ s/(?<=.)(?=(?:.{3})+\z)/,/g;
  [download]

• perlre and perlretut

Update: Tested. Fixed. I knew I needed that \z.
Update: Added third solution, a simplification of the second.