The MMU knows whether a page is present in physical memory or not thanks to the "present" bit in page-table entries. 

If a process references a page that is currently stored on disk, the process makes a read syscall to read the page from disk.

If the memory image of a new process does not fit in physical memory, the process is always terminated by the OS. 

If a process references a page that is currently stored on disk, the MMU triggers a page fault, which causes the OS to map the page to a frame in physical memory.