Average times calculated by the best times from each driver in the two 20 minute sessions determined the grid for Sunday's 500km encounter.
Storey qualified fourth in the opening 20 minute session for professional drivers before co-driver Hackett topped Q2 with a 1:28.38s effort, which gave the duo an average of 1:27.851s.
“We haven't done the sprint rounds and I didn't think it was going to be an issue,” said Storey.
“Pole position doesn't really matter over the course of a race, but it does give us confidence tomorrow that Peter is the fastest of his group and has the speed advantage on them, while I am up with the top professionals.
“It does mean something in some respect.”
“It is incredibly close with four manufacturers in the top four places with about four tenths separating them,” added Hackett.
“In GT racing, the balance of performance as much as we complain about it is very close.”
A strong display from both David Russell and Roger Lago in the Lago Racing Lamborghini ensured four different manufacturers occupied the first two rows of the grid.
The top 10 was completed by Ash Samadi/Chris Pither (Audi), Steven Richards/James Bergmuller (BMW) and the Bathurst 12 Hour winning Maranello Motorsport Ferrari 488 of Peter Edwards and Graeme Smyth.
While delighted to score pole position, the Eggleston Motorsport Mercedes did so without the use of the newly permitted tyre tents.
The tents, which pre-heat the control Pirelli tyres, are used by the majority of the grid and have proven to be an advantage.
The team is now looking to secure the funds to secure the use of one to boost their chances in the race tomorrow.
“We are looking for a solution tonight,” said Hackett.
“We need 20 grand and we have 24 hours to find it. It would be better to have them, so we are trying to find a solution.
“It is not essential for the race but it will help. If you can be on the pace a lap earlier and not lose 10-15 seconds then its is worth it.”
The Australian Endurance Championship will complete a 10-minute warm-up ahead of the 500km race at 1340.
Results: Australian GT Endurance Championship Qualifying