The senior batsman continued his wretched run of low scores in the series when he was needlessly run out for four.
Samuels, who has scored a total of 35 runs in five innings in the series, hit towards point and darted off for a run only to stop in the middle of the pitch.
Batting partner Kraigg Brathwaite had dropped his bat before retreating to his end and Samuels was stranded by Josh Hazlewood's throw to the striker's end.
At the time of the onset of rain, the tourists were 115 for three in the 42nd over with Brathwaite unbeaten on 66.
The Windies also lost star batsman Darren Bravo during the middle session for 33 to a hook shot off James Pattinson.
Pattinson dug one in and Bravo top-edged to Usman Khawaja at backward square leg in the third over after lunch.
Bravo looked disconsolate at his dismissal on a flat wicket as he made his way from the ground ending a 91-run partnership with Brathwaite and opening up the Windies batting.
Shai Hope, recalled for injured opener Rajendra Chandrika, began positively with some crisp drives for threes but fell in the fifth over.
Josh Hazlewood got him to prod outside the off-stump and he was snapped up by Peter Nevill for nine.
Chandrika injured his groin in the morning warm-up following on from leg-spinner Devendra Bishoo injuring his shoulder on the morning of the second Melbourne Test.
Spinner Nathan Lyon was introduced into the Australian attack in the eighth over, indicating that spin was likely to make a significant impact over the course of the Test.
Fellow spinner Steve O'Keefe was brought on for his first bowl in the 27th over to applause from his home crowd at the Sydney Cricket Ground (SCG).
It is the first time two recognised spinners have bowled in tandem for Australia in a home Test for a decade.
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