The win was Ford's first at Mount Panorama since 1998 (Jason Bright and Steven Richards - Pirtek Racing). It was Lowndes first triumph in the race since 1996 and it was Whincup's first win in the 'Great Race'.
The win was Ford's sixth win of the season from nine rounds. It was Lowndes fourth win and Whincup's second.
In one of the most emotional-charged races ever held at Bathurst, Lowndes held off a determined Rick Kelly over the final laps to win by 0.01 of a second!
Rounding out the top-three was JELD-WEN Motsport's James Courtney and Ford veteran Glenn Seton.
The race itself was dramatic from the start with pole position winner Mark Skaife crashing on the opening lap. It set the tone for a race that had 10 safety car periods over the 161-laps.
Others to strike drama included the CAT Ford Performance Racing Falcon of Jason Bright and Mark Winterbottom, as well as the First Rock Home Loans Racing Falcon of Steven Johnson and Will Davison.
This resulted in an ever-changing leader board where teams gambled with fuel strategy.
The race settled down just after the half-way mark when Jamie Whincup and Todd Kelly battled for the lead. Whincup took first position from Todd Kelly on lap #109 and this proved a decisive part of the race as he handed the Falcon over to Lowndes with a 10-second lead.
Lowndes' lead was evaporated with just 10 laps to go when the final safety car was called onto the track.
Lowndes drove an inspirational final seven laps after the re-start to take the chequered flag.
It was an emotional Lowndes who along with Whincup took the first ever Peter Brock trophy.
"This is the biggest and most important win of my life," said Lowndes.
"It's been too long between victories for me at Bathurst and for the Ford fans it's been even worse.
"To get it for Ford, myself, Jamie and our awesome crew is just amazing.
"With all the emotion around Peter Brock's passing and the pre-race ceremonies honouring him today, I was just so determined to win this race. I'm so proud to have my name on the Peter Brock trophy.
"I have to say that Jamie was awesome today. He pushed me all weekend and in the race I was so confident in him doing the job and he didn't let us down. He's a wiz kid!
"We gave it everything in the race. Rick as always is a tough competitor and Todd was just as tough when he battled with Jamie. So to win against great competition like that you know you have done a great job.
"Our crew was fantastic. We kept to a plan with our pits stops. We made just four stops for the race, while others made up to eight! This gave us great track position to keep our place near the front.
"This result is great for our championship chase. Today shows that the best way to win a title is go out and try to win every time - especially at Bathurst."
After finishing second last year Jamie Whincup is now a Bathurst champion.
"It's the highlight of my life," said Whincup.
"I had a big responsibility for this race and I'm really pleased with how I drove. I drove the car as hard as I could and it remained strong.
"I have learnt so much this weekend to win this race. I know that it will hold me in a much stronger position not just for this race in the future but others races as well. Importantly I want more!
"I'm so pleased to win it for the team and the Ford fans. They have been awesome since I joined the Blue Oval this year and they showed all that emotion during the podium presentation.
"Now we all have something to really cheer about!"
Ford Motor Company President Tom Gorman enjoyed the celebrations.
"This is a major highlight in my three years that I have been at Ford Australia," said Gorman.
"I don't think I knew how much it meant until Craig crossed that line.
"The emotion and importance of this win can't be underestimated. I know everyone at the Ford Motor Company in Australia and indeed around the world will enjoy this result.
"For our dealers and fantastic supporters I'm especially pleased. They really deserve it. We have won every major trophy over the past three years - now we have the piece of silverware that everyone has been waiting far too long for.
"To Craig and Jamie, as well the entire Team Betta Electrical crew a big thanks. Together they have worked so hard to win this race. To be part of it is something I will never forget."
James Courtney showed that he has now well and truly arrived on the V8 Supercar scene. The JELD-WEN Falcon had its chances but couldn't quite match the pace of the two leaders.
"It definitely feels good to get a result in the biggest race of them all," said Courtney.
"It was the hardest race I have ever driven. I had to double-stint at the and my left-hand looked more like a cramped claw after all the gear changes!
"I had a lot of great battles today, including holding off my team-mate Russell Ingall. It's great to have a team that lets their drivers race it out.
"I've enjoyed working with Glenn and I have taken a lot from his experience in this race. Probably the best part has been seeing how his enthusiasm is still there after 23 starts."
Seton once again missed out on victory but was more than happy with the result.
"Not too many people have podiums at Bathurst, let alone wins," said Seton.
"To have the opportunity to drive with the Stone Brothers Racing organisation and a guy who has the talent to not just win this race but also a future championship has been a great experience.
"We went into the race with a dedicated plan and that included me starting the race. I took the challenge with both hands and really enjoyed today's race. My second stint was also very strong and I had a good feeling that James would put us in a position at the end.
"I'm so pleased for Craig to win today. He's not just the most appropriate winner to honour Peter Brock; he's also the class of this championship.
"This was the first time I've stood on the podium and been able to celebrate a Ford win! That was very exciting and the sea of blue was awesome. I'm sure we'll see more of that!"
The top-10 also included Caltex Racing's Russell Ingall and Luke Youlden in fourth, APVC Racing's Alex Davison and Grant Denyer in ninth and WPS Racing's Jason Bargwanna and Craig Baird in 10th.
The V8 Supercar Championship Series now heads to the Gold Coast in just two weeks time for the Indy Carnival. Craig Lowndes will go into that event as the hottest favourite after his Bathurst win as well as being the defending race champion.