Clarke chose to bat in heatwave conditions on a bouncy Perth pitch.
Expectations of a lively first session were on the mark as the home side reached 3-107 at the lunch interval.
Australia have lost the wickets of Chris Rogers (11), Shane Watson (18) and Clarke. The in-form Clarke was caught at short midwicket by rival skipper Alastair Cook in the second last over of the session.
Clarke's dismissal was a triumph for offspinner Graeme Swann who had struggled in the first two Tests which yielded four victims.
Clarke had been in sparkling touch with centuries in the Brisbane and Adelaide Tests.
Opener David Warner is 49 not out off 55 balls including seven fours and one six while Steve Smith is yet to score.
England's fans were in full voice in the second over as Rogers departed, run out after a direct hit from James Anderson at midwicket.
And the dismissal of Watson, caught at second slip off Stuart Broad's bowling, placed Clarke under heavy pressure at 2-52.
"That is a really poor dismissal. That shot is not on," ABC commentator Geoff Lawson said of Watson's exit.
Paceman Tim Bresnan dropped a difficult return catch off Warner on 37 and the aggressive opener crunched a four and a six later in the over as Australia reached their century.
However, Clarke's departure gave England the honours for the session.
Australia named an unchanged side while England recalled Bresnan for spinner Monty Panesar.
Cook is also playing his 100th Test.
"To be standing here playing my 100th Test is extremely special and for Alastair as well," Clarke said before play.
Cricket Australia chairman Wally Edwards presented Clarke with a commemorative 100th-Test cap before play on Friday.
Clarke's men lead the five-match series two-nil and will regain the Ashes if they win in Perth.
Australia's Ryan Harris, who is playing despite battling a chronic knee complaint earlier this week, is wearing a black arm band after the death of his grandmother Ouna Harris.
Offspinner Nathan Lyon has been retained after Australia had opted against an all-pace attack.
"What four quicks can't do, five can't. We need the spinner," Australian coach Darren Lehmann said.
A top of 38 is forecast for Friday with more heatwave conditions over the weekend which will dry out the pitch and possibly cause some cracking.
"It will take some turn as the game goes on," Lehmann said.
AUSTRALIA FIRST INNINGS
C ROGERS run out (Anderson) 11 9 9 2 0
D WARNER not out 49 118 55 7 1
S WATSON c Swann b Broad 18 41 29 3 0
M CLARKE c Cook b Swann 24 56 44 5 0
S SMITH not out 0 6 7 0 0
Sundries (4lb 1w) 5
Three wickets for 107
Fall: 13 (Rogers), 52 (Watson), 106 (Clarke).
Bowling: J Anderson 5-1-19-0 (1w), S Broad 7-1-39-1, T Bresnan 6-0-33-0, B Stokes 5-1-11-0, G Swann 1-0-1-1.
Batting time: 118 mins. Overs: 24.
Umpires: Billy Bowden (NZL), Marais Erasmus (RSA).