Summer signing Chery got his first goals in English football, netting shortly before and after half-time, and Austin’s 63rd-minute strike appeared to make the game safe for Chris Ramsey’s side.
But Rotherham hit back, with Jonson Clarke-Harris scoring with 18 minutes remaining and Tom Thorpe’s 87th-minute goal giving them hope.
However, Austin sealed victory for his side by slotting home from the penalty spot in injury time.
Former England forward Bowles, who has Alzheimer’s disease, looked in good physical condition as he was introduced to the crowd before kick-off on ‘Stan Bowles Day’, organised by the west London club as a tribute to the man widely regarded as its best-ever player.
The home fans greeted him with a standing ovation and were on their feet again four minutes before the interval when Chery rounded off a slick move by side-footing home after James Perch’s right-wing cross was nudged into the Dutchman’s path by Austin.
Striker Austin, who has been linked with several clubs in recent weeks, was also involved in the second goal, which arrived four minutes into the second period.
He found Massimo Luongo, who pulled the ball back from the right for an unmarked Chery to score.
And Austin got on the scoresheet himself when he cleverly moved away from three defenders and tried his luck from near the edge of the penalty area with a shot keeper Kelle Roos should have saved but allowed to squirm through him and into the net.
Clarke-Harris took his goal well, curling beyond keeper Rob Green from 20 yards after QPR midfielder Alejandro Faurlin had given the ball away.
Thorpe was then well placed to score from a few yards out when Danny Collins flicked the ball on after Rangers failed to clear a corner.
Rotherham had other chances – they might have taken an early lead when Clarke-Harris got away from Perch and crossed for Matt Derbyshire, who was unable to apply the finish from close range.
After Chery’s first goal, Green produced an important save at his near post after Lee Frecklington’s intended cross deflected off Rs defender Grant Hall.
And shortly after Chery’s second, Clarke-Harris missed a golden opportunity to make it 2-1 when he failed to connect properly with a header from Joe Newell’s left-wing cross.
Austin’s form will no doubt increase speculation that he will be snapped up by a Premier League club before the transfer window closes.
His goals capped an impressive display and, shortly after his first, he felt a penalty should have been given when he went down under a challenge from Collins.
When a spot-kick was awarded following Chris Maguire’s foul on substitute Sebastian Polter, Austin stepped up to score his fourth goal of the season.