use strict;
use warnings;

use Data::Dumper;

my @partTuples =
   (
      q{abc,1.1,apple},    # 1st element
      q{def,3.6,orange},   # no dups. so OK
      q{abc,1.5,pear},     # OK id only dup.
      q{abc,1.1,kiwi},     # dup. id and version
      q{ghi,1.2,peach},    # no dups. so OK
      q{xyz,1.1,plum},     # OK version only dup.
   );

my %seen = ();
my @uniquePTs =
   grep {! $seen{join q{:}, $_->{id}, $_->{version}} ++}
   map
   {
      {
         id             => $_->[0],
         version        => $_->[1],
         classification => $_->[2]
      }
   }
   map
   {
      [split m{,}]
   }
   @partTuples;

print Dumper(\@uniquePTs);

##</code><code>##

$VAR1 = [
          {
            'version' => '1.1',
            'classification' => 'apple',
            'id' => 'abc'
          },
          {
            'version' => '3.6',
            'classification' => 'orange',
            'id' => 'def'
          },
          {
            'version' => '1.5',
            'classification' => 'pear',
            'id' => 'abc'
          },
          {
            'version' => '1.2',
            'classification' => 'peach',
            'id' => 'ghi'
          },
          {
            'version' => '1.1',
            'classification' => 'plum',
            'id' => 'xyz'
          }
        ];