I'm not familiar with the term "System level program" per se, but if it's anything like "System level programming", then it has to do with writing fairly low-level code that interacts directly with a "system" (usually specific hardware/platform/architecture/etc) and abstracts it in some way (System Programming) to allow for Higher level programs to be written that can be system-agnostic.
Your question seems to be related to what is the difference between "system programming" and application programming. Functions like open(), printf(), etc assume the underlying system calls are present, and are, in a way, high-level. That said, the line between system-level and application-level programming is blurry, and has shifted up in many peoples minds. Many people now consider any program written in languages like C or C++ to be a system-specific program that is not portable, 15 years ago, that was not the case.
So, if you are asking what is the distinction between Application & System level programming, then you have a lot of reading to do. Look over the linked wikipedia article. It should give you a good starting point.