His Prodrive Racing Australia teammate, Chaz Mostert, was on course to win the race. The 23-year-old had been in control until lap 33, when he spun and crashed his FG X Falcon unaided.
Mostert had started from pole position and held his place off the line, only to surrender it to Lowndes on the second lap.
After getting the first of their pitstops out of the way, Mostert went on to pass Lowndes on lap 22 on the back of a tense nose-to-tail battle.
He leapt out to a comfortable 1.1s lead, but it all came undone after a mistake at turn four sent him into the dirt then onto a tyre barrier.
The crash triggered a safety car and sent him to the back of the pack after some necessary repairs.
"We were well and truly in control of that one," said engineer Adam DeBorre.
"We're still learning, he's still young, but [it's] disappointing not to get this one across the line.
"We'll work with him, analyse it, and give him a slap on the wrist if we need to - if not, pat him on the back."
It marked a disappointing end to what's been a stellar round for Mostert, who celebrated his new two-year deal with PRA with three pole positions, a race win and podium.
His slip-up left Winterbottom, Lowndes and Coulthard to battle it out up front.
Winterbottom was the best of the trio for the remaining laps, fending off a persistent Coulthard to claim race honours.
Reigning champion Jamie Whincup, desperate to make up ground after a poor start to the round, clawed his way up from 22nd to 10th. He is fifth in the overall standings.
The championship resumes in Darwin from June 19.
