This seems to do the job:

#!/usr/bin/perl -w
use strict;

my @header = ('h1','h2','h3'); # I already know the headings
my %values; # make a hash of hashes to remember the values

while (<DATA>) {
  chomp;
  my @columns = split /\|/;
  my $unique = $columns[1]; # h2 is the unique identifier
  @{$values{$unique}}{@header} = @columns;
}
__END__
val1|one|1
val2|two|2
val3|three|3
[download]

I assume that the @values was a typo and have changed it to @columns.

--
<http://www.dave.org.uk>

"Perl makes the fun jobs fun
and the boring jobs bearable" - me