Van Gisbergen set the fastest time in Saturday's Top 10 Shootout with a gutsy 2m6.3267s lap, putting the VIP Petfoods/ Lucas Oil Commodore on Pole Position for Australia's great race – the first Bathurst pole of his career.
The Lucas Oil duo continued to be on the pace for most of the race, with Van Gisbergen building a lead of more than three seconds in his final stint, and looked likely to win the race.
After making a quick fuel stop with 12 laps to go in the final safety car period, when Tim Blanchard hit the wall, Van Gisbergen stalled but was unable to re-start the car in pit lane because of the starter motor issue.
"It's just gutting really. We were going pretty well," Van Gisbergen said.
"We were in the mix from the beginning but we weren't that comfortable with the car early on. The VIP Petfoods/ Lucas Oil Commodore just got better and better the day went on and eventually we had the fastest car. It just wasn't to be."
The team worked feverishly to get Van Gisbergen back on track to finish the race and salvage vital championship points – the Kiwi crossing the line in 16th place despite dropping three laps.
Co-driver Webb was equally devastated, and has already turned his attention the next event, the Castrol Gold Coast 600.
"We needed that last safety car. We knew we had the car speed, we only needed a small amount of fuel but unfortunately the car stalled it coming out of the box and there was just too much heat in the starter motor after such a long day," he said.
"We'll go through everything and try and get rid of the black cats that we ran over, turn up at the Gold Coast and push on.
"I always enjoy the Gold Coast. TEKNO Autosports normally go pretty good there as a team. Shane and I were both quick there last year so together I'm hoping we'll come home with a couple of surfboards."
The Gold Coast 600 is the final event in the Pirtek Endurance Cup, taking place 24-26 October.
Van Gisbergen remains fourth in the V8 Supercar Championship with three events remaining.