Under the Migration Act 1958, a substantive visa is any visa other than a bridging visa, a criminal justice visa or an enforcement visa. In everyday terms it is the visa you hold or are applying for, as opposed to the bridging visa that keeps you lawful while an application is decided.
The difference matters in practice. To lodge a second Working Holiday visa in Australia, you must hold a substantive visa or have held one that expired less than 28 days ago. To be granted a Bridging visa B, you must have held a substantive visa. And an onshore partner visa applicant who does not hold a substantive visa must include at least 2 statutory declarations from Australian citizens, permanent residents or eligible New Zealand citizens.