If you can't get the first applicaiton to manipulate a lockfile or otherwise signal your script, you can use incron (a cron like utility for file system events) to signal your second script that it is safe to read.
I use incron to detect the close file event for any file in my public ftp submission directory and as soon as it is done being uploaded, incron launches a script that yanks it away to a non-public directory so that every individual's uploads are private to other users whithout giving everyone a different area.
I also have a web interface to reboot my server, turn on and off anonymous FTP, share or not share my media directories (on/off or for a timeout period), etc. I know very little CGI, so instead of handling it in CGI, I save the state of the user radio button clicks and password hash to a text file and use Incron to detect a change and launch a shell script which parses and interperates it. I did it out of ignorance of CGI but I believe it is very secure.