Coulthard stopped out on the track trying to limp a car home with a punctured front right tyre and Patrizi spun Jack Perkins around.
Paul Morris briefly held fourth on pit stop strategy but soon lost places to Lee Holdsworth, Courtney and team-mate Ingall.
Todd Kelly was controversially given a drive-through penalty, taking away his, and the team's, best result of the season, for over-taking the safety car at its second deployment.
Team Vodafone continued on to claim a race 1-2, ahead of Holdsworth, Ingall, Courtney, Johnson, Shane van Gisbergen, Steven Richards, Rick Kelly and Greg Murphy.
Local Bahraini guest driver Fahad Al Musalem stopped with a broken gearbox in the Team Kiwi Ford.
Andrew Thompson spun and stopped at turn 1 after the right rear tyre delaminated, triggering a safety car.
The dice between those three became hard fought with Courtney suffering for tyre grip but still plenty of power with Will Davison joining the fight by lap 26.
Whincup raced on to win from Ingall, Lowndes, Winterbottom, Richards, Todd Kelly, Courtney, Johnson, Morris and Davison.
Third lap into the first corner and Steven Johnson ran into the back of Todd Kelly, spinning the Jack Daniels Commodore.
Safety was called for Todd Kelly's expired Commodore, the car stopped on the circuit Rick Kelly and Cameron McConville made contact and spun while the bunched field at the restart allowed James Courtney to pass Winterbottom, then move into third by taking advantage of a slow-out-of-the-corner Russell Ingall who had just lost second to Lowndes.