I'd use the first two fields as a key to a hash, something like the following:

#!/usr/bin/perl -w
use strict;
use Data::Dumper::Simple;

my %first_two;

while (<DATA>) {
    chomp;
    my ($key, $remainder) = $_ =~ /([a-z]+\|[a-z]+)\|([a-z]+)/;
    if (exists $first_two{$key}) {
       $first_two{$key} .= ",$remainder";
    }
    else {
       $first_two{$key} = $_;
    }
}

print Dumper(%first_two);

__DATA__
aaa|bbb|ccc
ddd|eee|fff
ddd|eee|xxxxx
hhh|iiii|jjjjjj
[download]

Which gives:

%first_two = (
               'aaa|bbb' => 'aaa|bbb|ccc',
               'hhh|iiii' => 'hhh|iiii|jjjjjj',
               'ddd|eee' => 'ddd|eee|fff,xxxxx'
             );
[download]

There are probably many more elegant ways to do it, but that's just the first thing that occurred to me.

Cheers,
Darren :)