Lowndes, Winterbottom and Mostert led the pack for the opening 25 laps, with less than a second separating the trio before the first round of pitstops.
Winterbottom was the last of the three to get a new set of tyres, forcing him to slip behind stablemate Mostert. "We split the odds a little bit ... but it was awesome for Chaz," said the reigning Bathurst winner, who leads the championship by 101 points over Lowndes.
"He needed that for his confidence, it'll be pretty scary to see what he can do the rest of the year."
Mostert, 22, endured a poor start to the season, but has found some form in recent weeks, claiming four podiums in the past six races.
His triumph yesterday denied Lowndes a 16th win at the Western Australian circuit and the record for most victories at a single track.
The 39-year-old equalled Mark Skaife's tally on Saturday, when he took line honours in the second of the day's two 100km sprints.
The afternoon was miserable for a number of other drivers, with the abrasive, high-braking track wreaking havoc on their tyres.
The Mercedes of both Will Davison and Lee Holdsworth suffered punctures within a few laps of each other early in the race.
Drivers will enjoy a five-week break before the next round in Darwin from June 20.
- AAP