As already said, using PerlSwitches is likely the easiest method, but if you wanted to keep using PERL5LIB, PerlPassEnv should help (Apache, or rather the respective modules such as mod_cgi, mod_fastcgi, mod_perl, clean the environment, so you have to explicitly pass environment variables here).

(BTW, you should generally be able to set apache-wide environment variables in /etc/apache2/envvars, which is being sourced from the startup script (/usr/sbin/apache2ctl) — this way you wouldn't need to set them in your root shell.)