The tourists showed the benefits of some overnight soul-searching on the bouncy WACA deck after pitching too short on Friday.
Steve Smith (111) and Mitchell Johnson (39) fell in the first five overs on Saturday after Australia resumed on 6-326.
The home side had been in early trouble at 5-143 before Smith added 124 with Brad Haddin (55).
Johnson did not add to his overnight score and was caught behind in the second over as Stuart Broad claimed his third wicket of the innings.
Smith was initially given not out as paceman James Anderson appealed for caught behind, but the decision was overturned on review as replays showed an inside edge.
The 24-year-old hit 14 fours and two sixes in a five-hour knock of defiance.
Smith and opener David Warner (60) were the only two batsmen in Australia's top six to reach 25.
Ryan Harris (12) was caught at gully off Anderson at 9-354.
Lyon was struck on the helmet by a bouncer from Tim Bresnan but finished unbeaten on 17, adding 31 for the last wicket with Peter Siddle (21).
Anderson (2-60) claimed two of the four wickets to fall on Saturday while Stuart Broad was a stand-out with 3-100.
England's batsmen will be desperate to make Australia's bowlers toil in the hot sun, with the temperature reaching 42 at the WACA on Saturday morning.
England bowling coach David Saker was critical on Friday night of his side's tactics.
"We went to the short ball probably too much," he said.
Australia's tail wagged again on Friday, much to England's frustration.
"No doubt we let it slip. It's probably not the first time this series as well we've had them on the ropes, to a degree, and we haven't finished the job," Saker said.
England trail two-nil in the five-match series and defeat in Perth would mean Australia regain the Ashes.
Smith says the Aussies will learn from England's mistakes.
"They might have bowled a little bit short in patches. When we come out and bowl we're going to be a yard fuller than what they are," Smith said.
AUSTRALIA FIRST INNINGS
C ROGERS run out (Anderson) 11 (9)
D WARNER c Carberry b Swann 60 (77)
S WATSON c Swann b Broad 18 (29)
M CLARKE c Cook b Swann 24 (44)
S SMITH c Prior b Anderson 111 (208)
G BAILEY c Pietersen b Broad 7 (12)
B HADDIN c Anderson b Stokes 55 (100)
M JOHNSON c Prior b Broad 39 (62)
P SIDDLE c Prior b Bresnan 21 (36)
R HARRIS c Root b Anderson 12 (19)
N LYON not out 17 (25)
Sundries (6lb 3w 1nb) 10
Fall: 13 (Rogers), 52 (Watson), 106 (Clarke), 129 (Warner), 143 (Bailey), 267 (Haddin), 326 (Johnson), 338 (Smith), 354 (Harris), 385 (Siddle).
Bowling: J Anderson 23-5-60-2 (1w), S Broad 22-2-100-3 (1w), T Bresnan 23.3-4-81-1, B Stokes 17-3-63-1 (1w 1nb), G Swann 17-0-71-2, J Root 1-0-4-0.
Batting time: 477 mins. Overs: 103.3.
Umpires: Billy Bowden (NZL), Marais Erasmus (RSA).