You need to quote the expression used for the split.

my @arr = split /\Q$ele\E/, $var;
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BTW, you have $ele when you should have $sep, unless you plan on splitting on the "~" character. You did say in your question that you wanted split on the "|" character?

In this case you probably don't need the \E since you are quoting the entire regex anyway.

#!/usr/bin/perl
# vim: sw=4

use strict;
use warnings;
use Data::Dumper;

my $var = "21|23|24~|34|45|56~";

my @arr = split("", $var);

my $sep = $arr[2];
my $ele = $arr[8];

my @ar = split(/\Q$sep\E/, $var);

print Dumper \@ar;
bruce:1:~/tmp $ ./p.pl
$VAR1 = [
          '21',
          '23',
          '24~',
          '34',
          '45',
          '56~'
        ];
bruce:1:~/tmp $
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