Johnson rattled the Proteas with match figures 12-127 in the opening match on a bouncy and bloody Centurion pitch.
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But in Port Elizabeth, Johnson was restricted to match figures of 3-121 and the hosts romped to an easy win.
The flat wicket was a point of contention with the Australian camp which predicted the curator would prepare it to suit South Africa.
"It was a lot more batter-friendly compared to Centurion," Amla said ahead of the third Test in Cape Town.
"The wicket was vastly different. The one on Centurion was a lot harder and had a lot more variable bounce.
"For any team, when you've got variable bounce, it's a lot more difficult to face. This wicket was a lot more true and the pace was a bit slower as well."
It begs the question over how the pitch at Cape Town will play.
Traditionally it has assisted the fast bowlers with decent bounce.
"Newlands has been a happy ground for the Proteas over the last few years, but the Aussies are a good team," he said.
"Without a doubt, winning the second Test gives you a bit more momentum - a bit more confidence in the team; guys got hundreds and guys bowled well.
"It's a better situation to be in going into a series decider."