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sub dyn_replace {
  my ($replace) = @_;
...
  $replace =~ s/\$(\d+)/$groups[$1]/g;
  return $replace;
}

my $pat = qr/foo(\d+)bar(\d+)/;
my $rep = 'x$1y$2';
my $str = 'foo36bar47';
$str =~ s/$pat/dyn_replace($rep)/e;
print "$str\n";