On a muggy night at the half-empty Suncorp Stadium defender Milligan got his first goal for Australia three minutes before halftime although he was fortunate to score.
Milligan succeeded at the second attempt, hammering home a shot from a tight angle that was deflected off goalkeeper Markus Rihihina into the net after the defender had shouldered his first effort against the frame of the goal.
"I don't mind how it comes, it's my first goal for the national team," Milligan told ABC Radio. "I was lucky it fell nicely for me off the crossbar, it doesn't happen often."
Without most of their European-based players, Australia, who only needed a point to qualify, dominated for long spells and should have won by a more comfortable margin against their defensive-minded opponents.
The result meant Australia finished their Group B campaign with 11 points from six matches.
Meantime, Japan eased some of the pressure on coach Takeshi Okada with a 2-0 home win over Bahrain in their Asian Cup qualifier on Wednesday.
Both teams had already booked their places at next year's tournament in Qatar but victory meant Japan finished top of Group A and lifted the gloom after a poor run of results.
Striker Shinji Okazaki headed home after some excellent build-up play in the 36th minute before midfielder Keisuke Honda nodded a second in injury-time for World Cup-bound Japan.
"I was never that worried about the team," Okada told reporters. "We knew there would be no excuses tonight and we got the result we deserved." Japan, booed off the pitch after slumping to third place at last month's four-team East Asian championship in Tokyo, finished with 15 points from six games, three clear of Bahrain.
Okazaki was guilty of a shocking point-blank miss from a Shunsuke Nakamura cross moments before finding the net following a sweeping four-man move.
The influential Honda stooped to head home a second goal Japan's vastly improved performance merited after twice being denied by Bahrain goalkeeper Sayed Jaffar.
"I'd missed a few chances so it was relief to score one," said Honda. "I don't know what people would have said if I hadn't put one away. It was important to get the result and we have to keep this form going." Okada paid tribute to the CSKA Moscow midfielder.
"Honda brings something different to the team," said the 53-year-old. "He keeps things simple and tidy and his energy gave the team a real boost." Okada added: "Perhaps we should have taken our chances earlier and we got a bit bogged down in the second half but we stuck at it and got our reward, which is important." Bahrain coach Milan Macala, whose side missed out on a World Cup place after playoff defeat by New Zealand last November, had no complaints.
"It's a fair result," said the Czech. "You could see Japan were better. The difference in the level showed."
South Korea beats Ivory Coast 2-0
In London, goals from Dong-gook Lee and substitute Tae-hee Kwak gave South Korea a 2-0 win over Ivory Coast on Wednesday in a friendly at Loftus Road.
Lee gave the Koreans a fourth minute lead in front of a small crowd of their red-shirted fans at the home ground of English Championship side Queens Park Rangers.
Kwak sealed victory for the Koreans when he headed home Jae-sung Kim's corner in the 90th minute.
Ivory Coast, who fired coach Vahid Halilhodzic last weekend after a poor African Cup of Nations, controlled possession in the second half but failed to break through.
Captain Didier Drogba's 58th minute free kick gave the Africans' their best chance to equalize but Bakari Kone's close-range shot was saved by goalkeeper Jae-woon Lee.
England to play Mexico, Japan ahead of World Cup
England has confirmed it will prepare for the World Cup by playing Mexico at Wembley Stadium and Japan in Austria.
Although no date for the Mexico game has been finalized, it will be after England's first training camp at altitude in the mountains of Austria starting May 17.
Many of the World Cup games will be staged at altitude in South Africa, and England is one of several teams headed to Austria to get used to the conditions.
England's game against Japan will be at Graz on May 30. The team will arrive in South Africa on June 3 for the start of the tournament eight days later.
