The Hibernian forward got down to head in the crucial second goal for the Socceroos at the Khalifa International Stadium in Qatar, and he has now been directly involved in eight goals in his last eight internationals, scoring five times and providing three assists.
Australia snatched a ninth-minute lead when Awer Bul Mabil lashed home a left-footed strike.
Graham Arnold's side was then indebted to goalkeeper Mat Ryan, who kept it ahead with two fine saves, but he was beaten in the 28th minute as Al Mandhar Al Alawi pulled Oman level, sidestepping Harry Souttar and thrashing a shot high into the right corner.
Australia regained the lead in the 49th minute when Adam Taggart's shot was only parried as far as Boyle, who was deadly from close range.
The hard-earned success was sealed when Mitchell Duke side-footed into the left corner late on.
It means Australia has three wins from three in the third round of Asian World Cup qualifying, having won eight from eight in the second round, the stage at which the Socceroos began their campaign.
They become the first team to have won 11 games in a single World Cup qualifying campaign.
Australia has won 12 consecutive qualifiers in all, including the 3-1 play-off win over Honduras that took it to the 2018 World Cup.