With Australia leading 18-3 on the stroke of halftime in the 60-11 romp, O'Connor lined up a conversion attempt at Twickenham.
The youngster has a habit of lifting his foot as he prepares and when he did so this time Stringer raced out to charge down the kick.
O'Connor didn't start his run-up and the Irishman stopped on reaching the ball near the sideline.
Stringer glanced towards referee Romain Poite, then picked the ball up and ran off for the halftime break to the enormous delight of the home crowd.
O'Connor could only smile at the incident but the miss stopped him from producing a perfect nine from nine with the boot on the day.
"I think it was on the basis that he had moved which he had been doing routinely," Wallabies coach Robbie Deans said.
"It has happened on a number of occasions.
"But the referees have never allowed the charging player to go through with it but in this instance Romain did."
O'Connor had similar problems during last month's World Cup quarter-final in New Zealand.
However referee Bryce Lawrence ruled South African winger JP Pietersen had moved too early and the Australia was allowed a re-kick which he missed.