First, you are saving only one row. Fix it with something like:

  foreach $line ( <INFILE> )
  {
      if( $line =~ /^Name/ )
      {
        @columnNames = split(/\t/, $line);
     }
      else
      {
         push @rowValues, [ split(/\t/, $line) ];
      }
  }
[download]

Second, you are setting and/or incrementing the row and column indexes inappropriately (you also have an extraneous write right before the first loop); fix it with something like:

  $row = 0;
  $count = 0;
  foreach $element(@columnNames)
  {
    $worksheet->write($row,$count,$element);
    $count++;
  }

  ++$row;
  foreach my $rv (@rowValues) {
    $count = 0;
    foreach my $element (@$rv) {
      $worksheet->write($row,$count,$element);
      $count++;
    }
    $row++;
  }
[download]

Third, you are not using strict (q.v.), and are therefore heading for a world of pain.

Im normally a java programmer and cant seem to see a way forward...

If you think the problems with the code you posted had something to do with it being in Perl rather than Java I think you are missing the boat; the most serious errors in it are pretty generic.