The Nerang family was initially taken to Noumea after the crash on Monday due to the state of the elder brother, who suffered serious head injury and wasn’t fit to fly home.
His condition improved on Wednesday and was downgraded from critical to stable.
The seven-year-old suffered a broken leg, while his mother fractured her pelvis in the crash.
Queensland Ambulance senior operations supervisor Gavin Fuller said the boys were in a stable condition when they touched down.
“It was a smooth flight, and there were no problems,” he said.
Another ambulance spokesman said the woman was greeted by her brother at the airport and was in a comfortable position when she was taken to hospital.
Seven other Australians were taken to Brisbane hospitals this week following the head-on collision with a commuter bus at Vanuatu’s capital Port Villa.
A 76-year-old woman remains in intensive care at the Royal Brisbane and Womens Hospital after suffering significant fractures and lacerations, but is now listed as being in a stable condition.
The driver of the tourist bus was charged with dangerous driving causing death, according to Vanuatu’s Daily Post.
The group was visiting the island as part of a P&O cruise.
The Pacific Dawn cruise ship is set to dock back in Brisbane on Saturday morning.