Mostert’s crew had initially thought that lap would not be counted, such was the tiny margin between the Supercheap Ford crossing the control line and the stoppage.
All drivers except Dale Wood, who had caused the red flags by hitting the Turn 3 tyre wall, returned to the track for the final minutes, but none could improve.
That left Mostert 0.2723 seconds clear of Jamie Whincup, who had recovered from side-on contact with the Turn 11 tyre barrier five minutes from the end to briefly go to the top.
“[Engineer Adam De Borre] is a bit of a bearer of bad news, he always gets down about any iffy moments,” said Mostert of initially being told his time would not count.
“I saw the red when I got down towards Turn 1. Unless there was a bit of a miscommunication when the screen came up red and the flags came out, I’m not too sure, but I was going to fight it anyway on the radio.
“I got the monkey off the back, but its a bit late in the year,” he added of ending a pole drought that stretched back to August 2016.
“It’s fantastic. The car’s been pretty good in the wet in the last couple of rounds, but this place is so sketchy. I was obviously very lucky to get the time with the red coming out.
“I’m just really grateful. The guys gave me a good car in the dry yesterday and it’s still working in the wet. We’ll see how we go.”
Whincup was also happy with second as he attempts to close-down the 91-point deficit to points leader Fabian Coulthard, who qualified just 16th.
“We were hoping to go quicker and quicker at the end of the session, but at the end of the day we’re rapt,” said Whincup. “P2, front row for a wet race, that’s a good result for us.
“When we stopped for five [minutes under the red flag], the track filled up with water, all of the tyres cooled down, so no one was going quicker at the end there.”
Whincup admitted he was lucky to get away with only superficial damage from his contact with the tyre wall.
“It looks better than what it felt inside the car, I just belted into the tyres there,” he said.
“We’ll fix that, get it back out there, PD [co-driver Paul Dumbrell], I think he’s going to start and go from there.”
Brad Jones Racing enjoyed a strong session, with Tim Slade and Nick Percat third and sixth, while the Nissans of Michael Caruso and Rick Kelly line-up fourth and fifth.
Shane van Gisbergen managed seventh, while the Shell V-Power Fords of Scott McLaughlin and Coulthard recorded just 12th and 16th respectively.
Coulthard’s session including a spin down the Turn 11 escape road in which the rear of the Falcon narrowly avoided contact with the concrete wall.
“It’s not going to change our day,” said Coulthard of the lowly grid slot.
“Obviously it’s nice to qualify at the front, but these conditions today are just going to purely be a race of survival. “
Wet weather is expected to continue through the day, with the 300km opening race to take place from 1425 local time.