Bathurst once again put on a show, with battles all through the pack and the crash of the day from David Besnard, whose huge shunt at the end of Mountain Straight saw his car explode into a huge fireball.
There were multiple safety cars, including one for a wayward kangaroo and an ill official, with Lowndes and co-driver Mark Skaife having to queue three times in the pits.
"It was a bit closer than we had liked but we got there in the end," said Tander.
"This will give the team a lot of belief that we are going in the right direction.
"To win this weekend is amazing and fantastic for the team. We will get a lot from this but we still have work to do."
Lowndes said that having to queue at three pit stops wasn't the best look. "It's one of those situations in a team when you have got two fast cars that are circulating around the same time and position," said Lowndes.
"Every time we were in our pit window a safety car was called. I'm not sure how much time we lost but it was a fair bit. It is frustrating."
The Kiwi drivers - other than Fabian Coulthard, whose race ended early on - had a good day. Murphy led away from pole position at the start of the race but by the middle stages the car, driven by Simonsen, had slipped out of the top 10.
As Murphy clawed his way back into the top 10, race strategy worked to his advantage when a safety car was called when he made his final pit stop on lap 139.
Murphy was second at the final restart but could not keep the fast-closing Lowndes behind and had to settle for third.
"Third is a huge result," said Murphy.
"I didn't see it happening that way halfway through the race. I guess it's one of those deals where you never give up. We pounded it out there for those last two stints and it worked out.
"Tander and Lowndes were too fast today and we didn't have their pace. We have a little bit of work to do but it's awesome for the guys in the team and awesome for Pepsi Max - their first Bathurst and we are on the podium.
"It is so tough out there and you need to find a stable place to go play and I think I'm really starting to get that at KR (Kelly Racing) and I haven't had that for a long time."
For a while there it was looking very good for Stone Brothers Racing, with Kiwi pairing Shane van Gisbergen and John McIntyre.
After starting the race from the third row of the grid, Van Gisbergen was looking comfortable running in the top-five during the early stages of the race. McIntyre also looked very comfortable in the car until he was turned around by Marcus Marshall at Forrests Elbow and lost 15 places. The two fought back brilliantly, clawing their way back up to sixth by the end of the race.
As a result Van Gisbergen retains his third place in the championship behind Whincup and new series leader Lowndes.
"Things were looking okay until Johnny got turned around," Van Gisbergen said.
"I pushed hard and we recovered to some extent but I'm pretty disappointed with Marcus [Marshall]."
And McIntyre said: "Things were definitely looking good early on.
"We had plenty of pace and the car was feeling really good. We were really lucky today because the punt from Marcus could have ended our race.
"We never gave up and Shane probably deserved a better result but we did well enough to preserve his championship position."
"Well, that's Bathurst.
"We had good cars this weekend and the boys all did a great job," said team co-owner Ross Stone, "but as is the nature of this place, everything can be tipped on its head pretty quickly."
The 11th event of the V8 Supercars championship, the popular Gold Coast 600, will be staged on the streets of Surfers Paradise from October 21 to 23.
