Matt Giteau, who had his 21st birthday last week, replaced Larkham in the pivotal playmaking role a minute later. He was instrumental in Australia's recovery before limping off with a knee problem eight minutes from fulltime.
Skipper Gregan grubbered ahead from a close-range ruck and dived on the ball rolling in-goal in the 59th minute after Waugh had stripped the ball from Bryan Redpath at a lineout and run 25 meters to take play deep inside the Scottish quarter.
Lyons barged over from the back of a five-meter scrum in the 64th minute for Australia's third touchdown and an unbeatable buffer.
Scotland, rank outsiders after edging into the quarterfinals on a last-ditch 22-20 win over Fiji last weekend, dominated the first half, spending almost two-thirds of the half inside Australia's half.
The Scottish forwards stole three lineout throws from the Australians, who were missing lock and vice-captain David Giffin, a late withdrawal with a strained biceps.
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