G'day acondor,

Welcome to the Monastery.

Here's the basic logic I'd use to tackle this problem:

#!/usr/bin/env perl -l

use strict;
use warnings;

use constant { IP => 0, CMD => 1 };

use Inline::Files;

my %data;

while (<IPLIST>) {
    chomp;
    my ($host, $ip) = split /,\s+/, $_, 2;
    $data{$host} = [$ip, []];
}

while (<CMDLIST>) {
    chomp;
    my ($host, $cmd) = split /,\s+/, $_, 2;
    push @{$data{$host}[CMD]}, $cmd;
}

for my $host (sort keys %data) {
    print "Connect to '$host' at '$data{$host}[IP]'";
    print "\tRun command '$_'" for @{$data{$host}[CMD]};
    print "Disconnect from '$host' at '$data{$host}[IP]'";
}

__IPLIST__
HOST1, 10.10.10.101
HOST2, 10.10.10.102
HOST3, 10.10.10.103
__CMDLIST__
HOST1, CommandA
HOST1, CommandB
HOST2, CommandC
HOST3, CommandD
HOST3, CommandE
HOST3, CommandF
[download]

Output:

Connect to 'HOST1' at '10.10.10.101'
    Run command 'CommandA'
    Run command 'CommandB'
Disconnect from 'HOST1' at '10.10.10.101'
Connect to 'HOST2' at '10.10.10.102'
    Run command 'CommandC'
Disconnect from 'HOST2' at '10.10.10.102'
Connect to 'HOST3' at '10.10.10.103'
    Run command 'CommandD'
    Run command 'CommandE'
    Run command 'CommandF'
Disconnect from 'HOST3' at '10.10.10.103'
[download]

Note that I have shown the logic related to your question but I have totally ignored the I/O: input dummied up using Inline::Files; output to STDOUT rather than appending to a logfile.

You'll need to write the code for the I/O yourself; however, the way you're currently doing this if far from optimal. You should use lexical filehandles, the 3-argument form of open and error checking (possibly using the autodie pragma).