You could just open and write the last one at the end. This should also fix your numbering problem.

 
open(INPUTFILE, "$file");
open(OUTPUTFILE, ">$outputfile");
my $counter = 1; 
while (<INPUTFILE>) { 
   print OUTPUTFILE "$counter. $_";
   $counter++;
}
close(INPUTFILE); 
close(OUTPUTFILE);
[download]

If you want to copy over the old file, just do it at the end.

UPDATE: You should probably check to make sure the files actually open (using die) like you did in your original code.

UPDATE2: Only now does command line register in krujos' head. Doh!