I know that in a DOS/Windows application, you can issue system commands from code using lines like:
system(\"pause\");
or
s
Not surprisingly, the command is still
system("whatever");
and the header is still stdlib.h. That header file's name means "standard library", which means it's on every standard platform that supports C.
And yes, calling system() is often a bad idea. There are usually more programmatic ways of doing things.
If you want to see how lsmod works, you can always look-up its source code and see what the major system calls are that it makes. Then use those calls yourself.
A quick Google search turns up this link, which indicates that lsmod is reading the contents of /proc/modules.