Perl's list constructors flatten empty lists and arrays when building new lists. As LanX has written, there is no such thing as an "empty" element. You may define a placeholder value (e.g., undef or the empty string) for the use of your own application along with a custom parser (or maybe YAML/JSON/Text::CSV as LanX suggested), but that's as close as you can get.

c:\@Work\Perl>perl -wMstrict -le
"use Data::Dump;
 ;;
 my @ar    = (99, 88);
 my @empty = ();
 ;;
 my $ar = [ 1, @ar, 2, @empty, 3, (), ,,,,, (), (),(), 4 ];
 dd $ar;
"
[1, 99, 88, 2, 3, 4]
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