like so?

use warnings;
use strict;

use Data::Dumper;

my %hash = ();
my @array = (1,2,3};
my $href = \%hash;

for ( @array )
{
  $href->{$_} = {};
  $href = $href->{$_};
}

print Dumper (\%hash);
#'1' => {
#         '2' => {
#                  '3' => {}
#                }
#       }
[download]