From what I've gathered asking around, there is no way to pass back a perl array into a php script using the exec function.
The suggestion is to just print out your perl array variables at the end of your script, and then grabbing each array member from the array returned by the exec function. If you will be passing multiple arrays, or if you need to keep track of array keys as well as values, then as you print each array or hash variable at the end of your perl script, you should concatenate the value with the key and array name, using an underscore, as in:
foreach (@array) print "(array name)_(member_key)_($_)" ;
Then you would simply iterate through the array returned by the exec function, and split each variable along the underscore.
Here I like to especially thank Marat for the knowledge. Hope this is useful to others in search for similar answer!