Here's some example code on how to do this with a few tests. I'd invite adding some more tests and any bug reports/security issues as I've not really thought about this from a security perspective yet. It's a bit slower in that it matches twice, but it completely avoids any eval. 

use strict;
use warnings;

sub substitute
{
    my ($string, $from, $to) = @_;

    $from = qr/$from/ unless ref $from and ref $from eq 'Regexp';
    my @a = $string =~ $from;
    $to =~ s/\$(\d+)/$a[$1-1]/g; # was $to =~ s/\$(\d+)/\Q$a[$1-1]/g;
    $string =~ s/$from/$to/;
    $string;
}

my @tests = (
             [ "this is some test", "(is) s(o)me", '$1 n$2t a' ],
             [ "this is some test", "is some",   'is not a' ],
            );

for my $t (@tests)
{
    print "[$t->[0]]...";
    print "[",substitute(@$t), "]\n";
}

[download]
prints out: 
[this is some test]...[this is not a test]
[this is some test]...[this is not a test]

[download]
which is what I expected. But, as you can see, it's not a very extensive test, so feel free to try a few more.

Update: It turns out that the \Q in the $to replacement wasn't needed.

In reply to Re: How to do regex backreferences within $variable replacement text? by Tanktalus
in thread How to do regex backreferences within $variable replacement text? by ManFromNeptune

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