But he will want to take as many points as possible from Sunday's second race at Sandown to the final two races in Sydney next month to avoid Lowndes taking the title to the wire.
Wet weather specialist Kelly also produced a phenomenal drive as he so often does in the rain, leading a Holden 1-2-3.
He beat James Courtney, with Kelly's brother Todd completing a big day for their Jack Daniel's Racing team with third place.
Lowndes had struggled badly in the morning's wet 20-minute qualifying session - producing his worst qualifying run since 2004.
Whincup qualified second and looked capable of wrapping up the title this weekend.
But Lowndes let loose during the race and, 26 laps into the time-shortened 37-lap event, he passed Whincup with a flourish and climbed even further to sixth as his teammate slid through the field.
While they were slugging it out, Kelly started from pole and never relinquished his advantage in the pouring rain.
- AAP