use File::Copy; # for move()
open my $of, '<', $old_file or die "Can't read $old_file: $!";
open my $nf, '>', $new_file or die "Can't write $new_file: $!";
my $line_number = 0;
while (my $line = <$of>){
    chomp $line;
    print $nf $line, $list[$line_number];
}
close $nf;
close $of;
move $new_file, $old_file;