Teenage opener Sam Konstas went for single figures for the second time in a tough return Test and Cameron Green's struggles at No.3 continued as Australia went to stumps on day two at 4-92 in the second innings.
It means Australia hold a lead of 82 runs after their pacemen skittled West Indies for 190 in reply to 180.
The ongoing 27-run partnership between a newly patient Travis Head (13 runs off 37 balls) and Beau Webster (19 off 24) appears critical for Australia.
A total of 24 wickets have fallen across the first two days of the three-match series - Australia's final tune-up before the home Ashes this summer.
In the absence of injured talisman Smith, hoping to return in the second Test, Australia's top four managed only 47 runs between them to put pressure on the lower order on day three.
Konstas's highly anticipated comeback Test will finish with scores of three and five, but he was fortunate to have scored at all on Thursday (Friday morning AEDT).
The talented teenager was dropped twice from the bowling of Shamar Joseph (1-15) in the space of three balls during the second over before he had gotten off the mark.
Australia's familiar tormentor Joseph finally had his man when Konstas chopped on, the ball ricocheting from the toe of his bat and onto middle stump.
Green could also count himself lucky not to have gone sooner than 15 - still his highest score from four digs since being bumped up to No.3.
The towering West Australian successfully overturned the umpire's lbw call on 13, and added only one run before surviving Justin Greaves' review for lbw.
For the fourth time in as many Test innings since returning from a back injury, Green edged to the slips cordon after an uncomfortable stay at the crease - this time falling to Greaves.
Smith's injury replacement Josh Inglis (12) went cheaply for a second time this Test, shouldering arms and allowing Jayden Seales (1-24) to nudge off-stump with a peach.
Usman Khawaja's luck from the first innings also ran dry on 15, with ball-tracker inconclusive as the veteran fought to overturn the on-field call of lbw from Alzarri Joseph (1-16).
Earlier, West Indies' Roston Chase (44) survived an Australian lbw appeal on one and a Konstas dropped catch at square leg on four to forge a 67-run stand with Shai Hope (48).
But Chase looked hugely frustrated early in the afternoon session when he was given out lbw to Pat Cummins, convinced that he'd got an inside edge.
The Ultraedge review gave no clear evidence one way or another and the disgruntled captain had to go.
Hope would have been similarly disappointed to have been given out when replays cast doubt as to whether the ball had grazed the turf on its way to Alex Carey from Webster's bowling (2-20).
The familiar triumvirate of Mitchell Starc (3-65), Josh Hazlewood (2-34) and Cummins (2-34) all chipped in, while Nathan Lyon grabbed the final wicket of the innings, tempting Seales to slog one straight down Webster's throat in the deep.
9°C