#! /usr/bin/perl
use warnings;
use strict;

my %alphanum;
open my $COMMA, '<', 'file2.in' or die $!;
while (<$COMMA>) {
    my ($social, $id) = (split /,/)[1, 2];
    $alphanum{$social} = $id;
}

open my $VBAR, '<', 'file1.in' or die $!;
while (<$VBAR>) {
    chomp;
    my $social = (split /\|/)[1];
    if (exists $alphanum{$social}) {
        print "$_|$alphanum{$social}";
    } else {
        print "$_\n";
    }
}
[download]

John|123
Jane|456
John|123
Jane|456
Jack|789
[download]

John Doe,123,a0
Jane Smith,456,b1
[download]