Lowndes, who has just signed a new three-year deal to remain at Team Vodafone, stressed the importance of starting the season well after finishing so strongly in 2011 only to just miss out to Whincup.
Six of the past 13 V8 Supercar champions have also won in Adelaide the same year, with Whincup's three titles all coming off the back of Clipsal 500 wins.
"I was hoping to pick up exactly where I left off. Clipsal is the hardest event of the year and it's so important to get off to a good start,'' Lowndes said.
"At the end of last year, we were up and running and now we've hit the ground running.''
Four-time Clipsal 500 winner Whincup missed the front row of the grid at Adelaide for the first time since 2006.
But the defending champion remains confident he can catapult himself from the third row to a big performance in both Saturday's and Sunday's 250km races.
"The car was a bit fiery today but we're still in a good spot, so I'm happy with that,'' Whincup said.
Holden Racing Team's James Courtney was the highest-profile casualty of qualifying, failing to make the top-10 shootout.
He will start from 13th place on Saturday.
Davison's Ford Performance Racing team-mate Mark Winterbottom will start from seventh on the grid despite taking a broken left leg into the weekend's racing.
Winterbottom showed no ill affects of breaking his leg eight weeks ago in a waterskiing accident.
He was the quickest in two Friday practice sessions and early qualifying.
- AAP