Apache Permission Denied Error can be caused due to one of many configuration mistakes listed below

Check the apache configuration settings

i) The first is the reference to folder where cgi or perl files will reside and its execute permission settings

 <ScriptAlias /cgi-bin/ /usr/local/cgi-bin/>
 <Directory "/usr/local/cgi-bin">
     AllowOverride None
     Options +ExecCGI -MultiViews +SymLinksIfOwnerMatch
     Order allow,deny
     Allow from all
 </Directory>

ii) The second is the proper add handlers that are set for the file execution

AddHandler cgi-script .cgi .pl
<Files ~ "\.pl$">
    Options +ExecCGI
</Files>
<Files ~ "\.cgi$">
   Options +ExecCGI
</Files>

Check the apache error log for any messages (/var/log/apache2/error.log).