It's a fairly broad, open ended question. As you've framed the question, the answer is a simple yes.
There are lots examples of applications that are already written and PHP can use the system command to invoke applications that don't require PHP's overhead.
Further, PHP is open source so if you wish, you can write modules that you can include in your PHP installation.
Of course, there is some reason that you are asking this question. Maybe PHP isn't fast enough for you? Invoking system calls or writing modules may not give you the improvements you're looking for. Maybe you already have an application and don't wish to rewrite it but you need to include it into your system? System calls will work fine. Maybe you're just more comfortable in C/C++? Sure, making system calls will work fine. Maybe you're just asking because you're curious about PHP's abilities? It's very flexible... but whether or not it's a good way to proceed for you depends on how you wish to implement it.