I like your solution for replacing the nth occurrence of a character within a string. I don't know whether the following is a 'better suggestion,' but what about initializing $n (for the nth) to the desired occurrence:
use strict;
use warnings;
# Replace second comma
my $n = 2;
my $str = 'a,b,c,d';
$str =~ s/(,)/!--$n ? '|' : $1/ge;
print $str;
Output:
a,b|c,d
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