Whincup set a lap time of 1m 56.6623 seconds with Ford Performance Racing's Mark Winterbottom responding with a 1m 56.8156 on the Albert Park Circuit.
Jamie Whincup has continued Red Bull Racing Australia's progress of the MSS Security V8 Supercar Challenge at Melbourne's Albert Park Circuit topping the time sheets in the second practice session of the weekend.
Alex Premat was the third fastest with a time of 1m 57.0633 ahead of Craig Lowndes and fellow Fujitsu Racing driver Scott McLaughlin.
Tony D'Alberto finished the session in sixth with the Tekno Autosports duo of Shane van Gisbergen and Jonathon Webb in seventh and eighth respectively.
Todd Kelly was ninth in the first of the Nissan Altimas while Will Davison rounded out the top ten in the second of the FPR Falcons.
Despite being the fastest man heading into qualifying Whincup feels the full potential of his rivals is yet to be shown.
"I don't think everyone maximised their lap," Whincup said.
"That was my first time on the soft tyre in this car so it was all a bit of experimenting.
"The car really hooked up and the new tyre gives a really good feel through the car," he added.
Qualifying for race one of the MSS Security V8 Supercar Challenge takes place at 6:30 AEDT this evening.