The home side was 70 for one at lunch with Joe Burns not out 27 and the fit-again Usman Khawaja on 18.
Windies captain Jason Holder won the toss and sent the Australians into bat on a greenish MCG pitch, but a combination of attacking batting and wayward bowling negated any advantage the tourists might have had on winning the toss.
Warner crashed boundaries off Kemar Roach's first three balls before plundering 15 off his opening over.
Samuels took three grabs at the ball before taking the catch for a crucial wicket for the Windies, removing Warner for 23 off 12 balls.
The West Indies steadied the scoring rate as Burns and Khawaja put on 41 runs up to the lunch break.
The start of play was delayed by rain for an hour with session times to be adjusted to make up for the later start.
Australia left out Shaun Marsh for the return of fit-again Khawaja, while uncapped paceman Scott Boland was released from the squad.
It was an otherwise unchanged side for the showpiece Boxing Day Test with Australia favoured to retain the Frank Worrell trophy against the struggling tourists.
That looks on the cards after the Windies were thrashed by an innings and 212 runs inside three days in the first Test in Hobart. They last won a Test in Australia almost 18 years ago.
Bishoo, who had been in line for a return to the team, fell heavily while fielding during practice and was sent to hospital for scans on his left shoulder.
The Windies gave bowling allrounder Carlos Brathwaite his Test debut, following a tour-ending ankle injury suffered by paceman Shannon Gabriel in Hobart, in the only team change.
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