Don't reinvent the wheel, use Text::CSV_XS:

#!/usr/bin/perl

use warnings;
use strict;
use Text::CSV_XS;

my $csv = Text::CSV_XS->new();

while (<DATA>) {
    my $line = $csv->parse($_);
    print join("|",$csv->fields)."\n";
}

__DATA__
"00000142988AFA836117B1B572FAE4713F200567","9B3702B0E788C6D62996392FE3
+C9786A","05E566DF","J0180794.JPG",32768,3290,"WIN",""
"000005EE5E3F6961B78CE4549270DE5D05CBC0CB","8D025B6AE1994A40FCBB5AEC2E
+F273F9","5E8D7D42","WabIab, and more.bor",4760,4616,"WIN",""
"0000085FC602CD8AD4793A874A47D286DACB0F6A","8BA8BC04896C421A704282E9B8
+7B5520","8D89A85D","fpSDt,Finder,Link.gif",1161,2988,"Solaris",""
"00000FF9D0ED9A6B53BC6A9364C07074DE1565F3","A5D49D6DA9D78FD1E7C32D58BC
+7A46FB","2D729A1E","cmnres,pdb.dll",76800,1550,"WIN",""
[download]

OTOH, why do this at all? Commas within quotation marks are common enough in CSV files and (as you've found out) are easy enough to handle.