The Wallabies found themselves on the wrong end of a 15-8 penalty count, and referee Romain Poite sinbinned Scott Sio for collapsing a scrum in the second half of their 39-28 first test defeat in Brisbane on Saturday.
Australia, World Cup finalists last year, had looked set to extend their unbeaten four-match record against England in Brisbane when they took an early 10-0 lead from two tries.
England flyhalf Owen Farrell, however, kept the scoreboard ticking over with a succession of penalties and ended the game with six in total, claiming 24 points from the boot.
"Discipline is a big part," Fardy told Australian Associated Press in Melbourne. "That's what got England the game; six penalties they kicked - when you score four tries to two before the 79th minute and you're still behind, it's a disappointing thing."
Fardy said the biggest issues were at the breakdown, where they failed to adjust to Poite's decisions, and the scrum, where England re-established their dominance.
"We need to make sure with their 50:50s, if they're not on we're pulling out and not making bad decisions," Fardy added.
"I was guilty of a few of those when I thought I was doing the right thing but it turns out I wasn't."
The Wallabies may also look at making some tactical player changes for the clash in Melbourne after coach Michael Cheika gambled on a massive centre pairing of Samu Kerevi and Tevita Kuridrani for the clash at Lang Park.
Both struggled against a fast defensive line and scrumhalf Nick Phipps said the key to turning the English around may be to kick more. That could prompt the introduction of a playmaking inside centre to relieve the pressure on flyhalf Bernard Foley.
"We've definitely identified that we know that we've got to be a bit better at relieving pressure," Phipps said.
"There were probably opportunities in the game where we backed ourselves to use our feet a bit more than the ball in the air."
(Writing by Greg Stutchbury in Wellington; Editing by Peter Rutherford)
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