Everingham crossed the line just 0.2s behind Boys, having failed to start the Saturday race.
The top five runners were covered by just 1.8s, with rookie Matthew McLean and Declan Fraser finishing behind Jaylyn Robotham.
Boys and Feeney registered 279 points each for the weekend, with the former winning the round on a countback by virtue of his Sunday win.
Tickford Racing’s Zak Best finished third overall wth 240 points, ahead of Mouzouris, Matt Chahda and McLean.
Boys celebrates victory
The drama didn't end there; in the weeks after the Bathurst weekend, a post-event technical check found that the Walkinshaw Racing-built engine in Boys’ car exceeded the accumulated engine power number (AEP) by a factor which yielded a performance advantage.