roboticus++: Interesting, so at each iteration of the while loop it autovivifies the next key and you end up with a reference to the final memory location.

  # As long as we have multiple keys, access the next subhash
   while (@keys > 1) {
      my $key = shift @keylist;
      $hashref = $hashref->{$key};
   }
[download]

Should that be @keylist instead of @keys?

while (@keylist > 1) {
    my $key = shift @keylist;
    $hashref = $hashref->{$key};
}
[download]

Update: I just tried this and it doesn't work. $hashref = $hashref->{$key}; doesn't set anything in the hash and doesn't autovivify. I end up with an empty hash.

use strict;
use warnings;
use Data::Dump;
my %testhash;
my $hr = \%testhash;

my $count = 0;
while(<DATA>) {
    print "[", join('-',split ' ', $_), "]\n";
    add_val( $hr, ++$count, split ' ', $_);
}

dd \%testhash;

sub add_val {
    my ($hashref, $val, @keylist) = @_;
    die "Expected a list of keys!" unless @keylist;
    die "Expected a hashref!" unless "HASH" eq ref $hashref;

    # As long as we have multiple keys, access the next subhash
    while (@keylist > 1) {
      my $key = shift @keylist;
      $hashref = $hashref->{$key};
    }
    # Now set the value
    $hashref->{shift @keylist} = $val;
}

__DATA__
a1 a2 a3
jjj kkk lll mmm


Output:
[a1-a2-a3]
[jjj-kkk-lll-mmm]
{}
[download]

Update again: With the addition of the subhash from your update it works. Thanks.

Output:
[a1-a2-a3]
[jjj-kkk-lll-mmm]
{
  a1  => { a2 => { a3 => 1 } },
  jjj => { kkk => { lll => { mmm => 2 } } },
}
[download]