You have to replace:  if (/$re/) {...}

with :  while (/$re/g) {...}

-----

use strict;
my $re='.*?(@)((?:[a-z][a-z0-9_]*))(\\[)(\\d+)(\\])';

my @code = <DATA>;
my $code;
foreach (@code) {
    $code .= $_;
    while (/$re/g) {
        my $rndIndex;

        my $c1=$1;my $var1=$2;my $index=$4;my $c3=$5;

        $rndIndex = int(rand(99999));
        my $old = $c1.$var1.$index.$c3;
        my $varName = $index.$c3;
        $varName =~ s/$index/$rndIndex/; 
        $code =~ s/[$old]/$varName/g;
    }
}
print $code; #show output example

__DATA__
@a = ("'hello world'",'print ', ';');
eval(@a[1] . @a[0] . @a[2]);
[download]

Update: You don't have to capture "@", "[", "]"... plus several simplifications.

use strict;
my $code;
{
    #slurp mode (http://perldoc.perl.org/perlvar.html)
    local $/;
    $code = <DATA>;
}
my $re = qr {\@([a-z][a-z0-9_]*)\[\d+]};
$code =~ s{$re}{
    "\@$1\[" . int(rand(99999)) . "]"
    }eg;
print $code; #show output example

__DATA__
@a = ("'hello world'",'print ', ';');
eval(@a[1] . @a[0] . @a[2]);
[download]