Lowndes broke the previous mark held by Pepsi Max Crew's Will Davison in the prelude to the first race of the PIRTEK Enduro Cup Series.
Lowndes recorded a 1min08.9334 lap, four tenths of a second faster than the previous mark.
He was fastest in practice today ahead of Lee Holdsworth in the Irwin Racing Erebus Mercedes-Benz AMG, the first time the team has cracked the top three, and Davison.
Lowndes is driving with Warren Luff in the PIRTEK Enduro Cup, Holdsworth with the seasoned Craig Baird and Steve Owen with Davison.
Lowndes said the lap record had come as no real surprise, as much as he welcomed it.
"There is a couple of corners turn four, turn nine have been resurfaced and I think that getting better mid corner grip and actually getting out of those corners makes a big difference," Lowndes said.
"The new generation car with the independent rear end helps rides the curbs a bit better. At turn two and three we are able to smash through a lot cleaner than what we have been in the past.
"Also coming on to the main straight there has been a patch resurfaced it's not on the corner but in the drive out of the corner where it used to really bounce the cars.
"The track has improved, the cars are better and the teams have stepped up."
Holdsworth put to bed dramas around the Erebus Team in the leadup at Winton. All three Mercedes-Benz AMGs were extremely quick all day and constant figures in the top ten.
"I suppose it isn't surprising as we had a very successful test day last week," Holdsworth said.
"Our weakest point before this was green tyres and we worked on that at the test day and took a different direction and it worked. It's nice to feel what a green tyre feels like again with a bit of rubber underneath.
"I am hoping we can repeat it tomorrow, I don't want to get my hopes up too much."
Davison and Owen will be right up there tomorrow amongst the race favourites.
"It's always a fun lap around here," Davison said.
"It's been a great day, Steve was really fast in his session and I did drive round. I remember I did a nine-three in in 2012 and a nine-one in qualifying last year but I had a feeling that someone may be able to top it. But the day got better and better for us."
No less than eight drivers broke the previously standing 1min09.3670sec practice record.
Rounding out the top 10 were Scott McLaughlin, Alex Premat, Mark Winterbottom, Garth Tander, Alex Davison, Jason Bright and David Reynolds.
Championship leader Jamie Whincup came home 18th while Fabian Coulthard, also in the Championship hunt, was 19th.
A final practice session follows tomorrow morning at 10.20am AEST, for all drivers. A qualifying session, co-drivers race and main series driver race follows to determine the starting positions for Sunday's race, the first of the PIRTEK Enduro Cup.