Holden swept the podium with four-time champion New Zealander Greg Murphy and Dane Allan Simonsen finishing third.
Mark Winterbottom and Steven Richards were next in the highest placed Ford.
Tander's battle with Lowndes wasn't the first time he emerged on top against a TeamVodafone Commodore having endured a battle with Jamie Whincup earlier in the race.
But Whincup's race turned into a disaster when his Commodore lost power early in the 138th lap.
The three-time Bathurst champion limped his way around to the garage for repairs but his bid for another victory was over.
His 21st-place finish also means he falls 100 points behind Lowndes in the V8 championship standings with four rounds remaining.
Ford driver David Besnard had a lucky escape after a spectacular crash on lap 112 left his Jim Beam Racing Falcon engulfed in flames.
Besnard hit a tyre bundle hard on his first lap after a pit stop, rupturing his fuel tank and spilling fuel all over the track.
The spill ignited and surrounded Besnard's vehicle but quick-thinking marshals doused the inferno and the 34-year-old part-time driver emerged unharmed.
Holden rookie Cameron Waters, 17, also hit a wall and had a lengthy spell in the pits but he got back onto the track to become the youngest finisher at a Bathurst 1000.
The next V8 Supercars event is the Gold Coast 600 on October 22 and 23.
- AAP