But Khawaja was also in the middle when Mitch Marsh was controversially given his marching orders on day five.
South Africa successfully reviewed an lbw shout from Kagiso Rabada, with the ball-tracking replay suggesting the reverse-swinging Kookaburra would have clipped leg stump.
Skipper Steve Smith joked the verdict showed Rabada had started to bowl leg spin, while Khawaja questioned the accuracy of the ball-tracking replay long before Michael Clarke, Mitchell Johnson and Mark Waugh did.
"I knew there was something not right. I walked straight up to (umpire) Aleem Dar and said 'look, the contact point of where it actually hit and where HawkEye is saying it hit is just off'," Khawaja told radio station FIVEaa.
"The South Africans were as surprised as anyone that was given out. I walked past a couple of them and you can always tell when they're being sheepish and they know they've got one away."
Khawaja added it wasn't the first time a ball-tracking replay had delivered a surprising reading.
"I've had an issue with ball tracking, even in places like Sri Lanka and India where the ball spins a fair bit," he said.
"I don't think the ball accounts for the spin and swing really as well as we know what it does.
"It doesn't just happen against us. I'm sure we've got a couple that have been a bit dicey, you always remember the ones that go against you."