The 26-year-old inherited the lead on lap 12 when Michael Caruso, also on the soft tyre, pitted for fuel, and held the number one position until lap 17, when Kelly pitted for fuel and switched to four harder compound Dunlop tyres.
Kelly returned to the track in seventh position, but moved gradually up the order in the final half of the race to finish in a strong fourth position.
Brother and team-mate Todd Kelly had a mixed day, putting the #7 Jack Daniel's Racing Holden Commodore in the Top 10 Shootout for the second-consecutive event.
Todd Kelly, starting from ninth on the grid, broke a rear axle as he launched off the line at the start, the added grip of the softer compound tyre, which he was also starting the race on, a contributing factor in the failure.
Todd Kelly limped his Jack Daniel's Commodore back to the pits and retired, his soft tyres still in as-new condition for tomorrow's 67-lap race.
Craig Lowndes won today's fifth race of the championship at Winton, ahead of Jamie Whincup and Steven Richards.
JACK DANIEL'S RACING QUOTEBOARD
Rick Kelly - #15 Jack Daniel's Racing Holden Commodore:
QUESTION: Fourth is a great result in what was a very hectic race - and you're the top Holden.
"To be honest, I actually made a couple of mistakes as well," said Rick Kelly.
"Our strategy was to make sure we got one really solid result, and we said that a solid result for us was top five.
"We've been able to do that on the first day of the weekend so as a team, Jack Daniel's Racing has done a fantastic job.
"But when you finish fourth it's always extremely frustrating because you're so close to getting a podium and it would have been fantastic to get the first ever podium for Kelly Racing here today.
"Not to worry - we should be happy with the job we've done and we'll do our very best to make sure we're in the top 10 again tomorrow.
"We want to come out of this event being in the top five in the championship and we're working towards that quite well.
QUESTION: Having done one race with the new 'option' tyre in the equation, is the strategy any clearer now for the team?
"Because we finished the race on our hard compound tyre we've learned a lot that's going to help us tomorrow and certainly help Todd as well.
"So we should be extremely happy with third, the way today played out for us and the strategy ... we spent hours and hours constructively arguing in the truck about what strategy we should use.
"I think we've put the work in and this result reflects that."
Todd Kelly - #7 Jack Daniel's Racing Holden Commodore:
QUESTION: What happened at the start there?
"As soon as I took off the rear axle broke, about four metres into the start it started to spin one wheel," said Todd Kelly.
"So I just pulled straight off onto the grass and took off again on the grass again, to make sure it wasn't anything stupid like the gearbox jumping in and out of gear.
"It was definitely the axle so I just drove around and parked it, which is a shame because we would have ended up with a really good result there.
"We certainly needed those points and we've ended up with zero so it's disappointing.
QUESTION: Did the broken axle have anything to do with the extra grip of starting on the softer ‘option' tyre?
"Yeah, 100 percent. It would have never broken an axle with the tyre we've been using in the past, so its obviously something we need to look at.
QUESTION: Can you still use your option tyres in tomorrow's race?
"Yeah, they're still brand new."
RESULTS: Winton Race One
Race 5 of the 2009 V8 Supercar Championship Series
1. #888 Craig Lowndes 33 laps
2. #1 Jamie Whincup
3. #6 Steven Richards
4. #15 Rick Kelly
5. #14 Cameron McConville
6. #9 Shane Van Gisbergen
7. #22 Will Davison
8. #2 Garth Tander
9. #39 Russell Ingall
10. #34 Michael Caruso
DNF #7 Todd Kelly 0 laps
RESULTS: Top 10 Shootout
1. #5 Mark Winterbottom 1:23.0906
2. #2 Garth Tander 1:23.1564
3. #888 Craig Lowndes 1:23.1677
4. #1 Jamie Whincup 1:23.4585
5. #111 Fabian Coulthard 1:23.4591
6. #34 Michael Caruso 1:23.5985
7. #18 James Courtney 1:23.6198
8. #33 Lee Holdsworth 1:23.6836
9. #7 Todd Kelly 1:23.7534
10. #6 Steven Richards 1:23.8460
RESULTS: Saturday Qualifying
1. #888 Craig Lowndes 1:23.3646
2. #6 Steven Richards 1:23.4261
3. #1 Jamie Whincup 1:23.4457
4. #33 Lee Holdsworth 1:23.4474
5. #18 James Courtney 1:23.4825
6. #5 Mark Winterbottom 1:23.5171
7. #111 Fabian Coulthard 1:23.5494
8. #34 Michael Caruso 1:23.6167
9. #2 Garth Tander 1:23.7006
10. #7 Todd Kelly 1:23.7100
11. #15 Rick Kelly 1:23.7797
