I would shove the information from the two files into a hash, then iterate over the details in a for loop. I've commented inline. Note the telnet portions are untested:

use warnings;
use strict;

use Net::Telnet;

my $ip_list = 'ip.list';
my $cmd_list = 'commands.list';

# use the three-arg form of open,
# and *always* check for problems

open my $ip_fh, '<', $ip_list
  or die "Can't open IP list $ip_list: $!";

my %hosts;

while (my $line = <$ip_fh>){
    chomp $line;

    # split the line into host and ip,
    # then put this information into the %hosts hash

    my ($host, $ip) = split /,\s*/, $line;
    $hosts{$host}{ip} = $ip
}
close $ip_fh;

open my $cmd_fh, '<', $cmd_list
  or die "Can't open CMD list $cmd_list: $!";

while (my $line = <$cmd_fh>){

    # append each command to an array reference
    # under each host in the hash

    chomp $line;
    my ($host, $cmd) = split /,\s*/, $line;
    push @{$hosts{$host}{commands}}, $cmd;
}
close $cmd_fh;

my $log = './log.txt';

open my $log_fh, '>>', $log
  or die $!;

for my $host (keys %hosts){

    # I think the instantiation of the object could
    # be done outside of the for() loop as long as each
    # session is closed, but I'm unsure

    my $telnet = new Net::Telnet (
            Timeout=>10,
            Errmode=>'die',  # you were missing a comma here
            Prompt => '/# $/i',
       );

    # extract the ip for the current host

    my $ip = $hosts{$host}{ip};

    $telnet->open($ip);
    $telnet->login('USERNAME', 'PASSWORD');

    # loop over the command array,
    # and do something for each one

    for my $cmd (@{$hosts{$host}{commands}}){
        if($telnet->cmd($cmd)){
            print $log_fh "$ip $cmd successful";
        }else{
            print $log_fh "$ip Unable to Connect";
        }
    }
}

close $log_fh;
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-stevieb