"I'm fitter than I have been in a long time and far better prepared than I was last year,'' said Skaife, who teamed with Lowndes to win at Phillip Island last year prior to their Bathurst triumph.
"It's a big ask for any driver to come in for two races - it's a little like Nathan Buckley making a comeback for a grand final.
"I'm not for a second thinking that last year's result immediately puts us in contention.
"We are coming into the two hardest races of the year and arguably the two most challenging tracks here and in the world. Anything can happen.''
Lowndes edged out Team Vodafone teammate Jamie Whincup by three-tenths of a second with his fastest lap.
The pair are locked in battle for the overall V8 Supercar title, and both endurance races count towards the championship.
Ford driver Mark Winterbottom had one of the more unusual practice laps of the day, hitting a rabbit as he careered around the picturesque Phillip Island track.
Qualifying sprint races will be held on Saturday to determine grid positions for Sunday's 500km race.