Use split.

my $field = 5;    # the field to compare

open(FIRST, "> $file1") or die "Can't open $file1: $!";
open(SECOND, "> $file2") or die "Can't open $file2: $!';
while (defined(my $first = <FIRST>) {
    defined(my $second = <SECOND>) or last;
    my @first = split(/\|/, $first);
    my @second = split(/\|/, $second);
    if ($first[$field] eq $second[$field]) {
        # mark match
    } else {
        # mark no match
    }
}
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It's possible to shorten that somewhat by list slicing split, but this'll do for now. Be aware that the first element of a list has an index of 0.