If both the programs are running on the same server, you can handle the scenario as follows:-

open two pipe files, say pipe_1 and pipe_2
Let C program uses pipe_1 pipe for writing and pipe_2 for reading
Let perl program uses pipe_2 for writing and pipe_1 for reading.

In this way both the program can talk each other.

If both programs are running in different servers then you can use sockets.