As far as I can tell, your code should work, but it's not very Perlish. You can easily lose the loop control variable there and clarify the happenings. chomp can remove the end-of-lines on an entire list at once. join is ideal for concatenating a list of strings. In all, I'd write this like so:

use constant PER_LINE => 20;

my @out;
do {
    @out = ();
    while(<FILE>) {
        push @out, $_;
        last if not 1 .. PER_LINE;
    }
    chomp @out;

    print PIPE join ",", @out;
    print PIPE "\n" if @out;
} until @out != PER_LINE;
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See Mark-Jason Dominus' excellent Program Repair Shop and Red Flags article series on Perl.com for many introductory pointers on writing good code.

Update: D'oh! Fixed a tiny but nasty thinko in the code.

Makeshifts last the longest.