The All Blacks snatched a 39-37 victory with a Jordie Barrett (25) try after the siren, having been given a five-metre scrum in front of the posts after Bernard Foley (33) was penalised for time-wasting as he made to kick the ball to touch.
The win at Docklands stadium ensured the All Blacks kept the Bledisloe Cup, the annual trophy contested by the trans-Tasman nations, for a 20th year in succession, while also leaving them top of the Rugby Championship table.
French referee Mathieu Raynal's contentious decision was criticised by Wallabies coach Dave Rennie, while rugby pundits across the globe felt the home side were hard done by.
However, Foster, who also confirmed midfielder Quinn Tupaea (23) would miss up to three months after being injured in a dangerous clean-out by Darcy Swain (25), defended Raynal, saying he had been very clear in his communication with Foley.
"When a ref warns a player two or three times and they don't listen then you put everything in your own hands," he told reporters on Friday.
"Let's not forget all we won out of that was a scrum - we didn't win the game. We won the game with our next play.
"Do you feel for them? 'Course you do. It's the first time that's happened in some ways.
"That's the nature of the beast. It's nice being on the winning side of it.
"Overall in the match, I feel we deserved to come out on the right side. We just did it the hard way."
Wallabies lock Swain was given a yellow card for the dangerous clean-out on Tupaea after cannoning into his legs, forcing the midfielder off the ground injured.
He was cited for foul play on Friday and faces suspension.
Tupaea suffered a ruptured medial ligament and a partial rupture of the anterior cruciate ligament in his knee.
Though a bitter pill for the young midfielder, Foster had initially feared he might be out for up to a year with a more serious injury.
"We will wait to see if it's operable or it rehabs," he said.
"I haven't had a good talk to him this morning but they're always disappointing."
The All Blacks will be forced to make further changes for the final Rugby Championship clash at Eden Park, with centre David Havili (27) ruled out after clashing heads with captain Sam Cane (30).
Cane also failed a head impact assessment to be forced out of the test on Thursday but may be fit for next week's clash.
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