The Australians, who won the first Test in Hobart by an innings and 212 runs, dismissed the visitors for 282 in the final overs of the fourth day after declaring their second innings on their overnight 179 for three with a 459-run lead.
The embattled Caribbean tourists resisted the Australian push with a spirited 100-run sixth-wicket stand between skipper Jason Holder and former captain Denesh Ramdin. But they quickly lost their remaining four wickets to crash to defeat 1.3 overs before the scheduled close.
Holder was out for 68 off 86 balls, while Ramdin chipped in with 59 off 90 balls in his best Test score for two years.
Australia swell lead to 459 in Windies Test
Lyon, Australia's all-time leading off-spin wicket-taker with 182, was named man of the match with seven match wickets, while all-rounder Marsh finished with four for 61 in the second innings.
"'Lyono' did what he's done so well for us this summer, got wickets for us at crucial times. He's bowled beautifully," said Australia skipper Steve Smith.
Smith said of Marsh: "I think when he's in a good rhythm he's as good as any of the bowlers around the country at the moment, and he hit that rhythm today."
Ramdin and Holder held the Australians at bay for 21 overs until Ramdin was caught behind by Peter Nevill off Marsh.
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It was the first century partnership of the series for the embattled Windies.
"I'm obviously proud of the way the guys showed some fight in this game," said Holder.
"I'm still disappointed we didn't put up a better fight but still credit to the way the guys played, especially Darren Bravo in the first innings and Denesh Ramdin in the second innings. I thought the bowlers tried (too)."
"A better effort in this game."
Skipper Holder's resistance ended in the final overs of the day as he drove Marsh straight to Josh Hazlewood at mid-off.
The wickets then quickly tumbled. Kemar Roach went for 11 and Jerome Taylor was last man out for a duck after skying Marsh to a sprawling James Pattinson at fine leg.
It was an improved effort by the outgunned West Indies. The last time they batted for more than 80 overs in both innings of an overseas Test was against England at Lord's in May 2012.
Yet they have still failed to pass 300 in eight Test innings against Australia this year.
Earlier, Australia's no-ball wicket curse continued when Bravo survived on 12 after he was given out caught behind, only to be saved by a front-foot no-ball by Hazlewood.
Pattinson had two wickets denied to him for overstepping on Sunday's third day, and it was the wicketless Hazlewood's turn on day four.
"We probably let ourselves down a little bit with the couple of no-balls taking the extra three wickets, probably takes a bit of time out of the game," said Smith.
"I was glad the way we finished off. Taking that wicket just before the new ball was crucial for us.
"I thought our energy, intent and all that in the field was probably as good as it's been this summer."
Australia dismissed top order batsmen Bravo, Rajendra Chandrika and Marlon Samuels after lunch.
Bravo, the first-innings top-scorer with 81, was caught behind off Peter Siddle for 21, and Chandrika's 130-ball vigil ended when he was trapped leg before wicket to Pattinson for 37.
Senior batsman Samuels continued his dismal tour when he prodded at Marsh and was snapped up by Nevill for 19.
Smith was on 70 not out when he declared at the start of the fourth day. He finished the year with the most Test runs of 1,474 at an average of 73.70.
Only Joe Root (1,372) was in a position, in England's current Test against South Africa in Durban, to overtake him in the final Test of the year.
The final Test of the three-match Australia-West Indies series gets under way in Sydney on Sunday.
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