if (grep /$line/, $awsLists )

Using perl, grep on the lines in the file not the filename. For example (using test data instead of your command output)

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

my $awsLists = '/ansible/awsLists';
my @awsLists = ();
if (-e $awsLists){
  open my $fh,'<',$awsLists or die "$!";
  @awsLists = <$fh>;
  close $fh;
}

my $cmd = 'aws ec2 describe-instances --filters "Name=instance-state-n
+ame,Values=running" | grep PrivateDnsNam$';
my @output = <DATA>;#qx/$cmd/;

open my $fh,'>>',$awsLists or die "$!";
foreach my $line (@output){
  chomp($line);
  if (grep /$line/, @awsLists ){
    print "$line found\n";
  } else {
    print "$line not found - added\n";
    print $fh $line."\n";
  }
}
close $fh;

__DATA__
test 1
test 89
[download]

poj

---

---

Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!

Titles consisting of a single word are discouraged, and in most cases are disallowed outright.

Read Where should I post X? if you're not absolutely sure you're posting in the right place.

Please read these before you post! —

• How do I compose an effective node title?
• How do I post a question effectively?
• Markup in the Monastery

Posts may use any of the Perl Monks Approved HTML tags:

a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr

You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)

	For:		Use:
	&		&
	<		&lt;
	>		&gt;
	[		&#91;
	]		&#93;

Link using PerlMonks shortcuts! What shortcuts can I use for linking?

See Writeup Formatting Tips and other pages linked from there for more info.