Experts next hope to explore the stacks with underwater cameras.
Melbourne University geomorphologist David Kennedy says the columns were likely preserved because the sea rose so quickly after the last ice age.
"It probably ran straight across the top of these things without managing to erode them away and knock them over," Associate Professor Kennedy told AAP.
The stacks were also slightly protected by an old sea cliff at the same water depth.
Stacks only occur where rock is soft enough to erode from a cliff, but at the same time hard enough to support a pillar.
Like the so-called 12 Apostles - which actually now number eight - the newly discovered underwater stacks were once part of a larger limestone sea cliff dating back 60,000 years.
The discovery was made by Assoc Prof Kennedy, PhD student Rhiannon Bezore and Deakin University's Dr Daniel Ierodiaconou during sonar mapping of the reef, which supports commercial fisheries.
The findings have been published in the US-based Journal of Coastal Research.
- AAP