The holding midfielder played one of his finest and most influential matches in the green and gold as the Socceroos overwhelmed the Gulf nation 2-0 in Sydney to get their World Cup campaign back on track.
Ange Postecoglou's men went into their seventh match in the final round of qualifying for a spot in Russia with patchy form and four draws on the trot that had them third in Group B behind Japan and Saudi Arabia.
With only two teams to reach the finals automatically, this certainly was a crucial match for the Socceroos despite Postecoglou's claim that it was no different to any other World Cup qualifier that had to be won.
Milligan, 31, was deployed as a central defender in last week's match against Iraq in Iran but was reinstated in midfield alongside Mile Jedinak against the UAE in Postecoglou's new 4-2-3-1 system because Massimo Luongo, the other defensive midfielder in Tehran, was unfit.
Milligan took to the job with gusto and his contribution was immense. He fetched and carried all night and gave a masterful demonstration of the holding midfielder's role.
He was the driving force of the team from the back and led by example, showing that he could well be a Socceroos captain one day.
He also played as if he had a point to prove. Not because he wanted to show that he is a midfielder and not a defender.
It was because he was annoyed by the way the team had been bullied by the Iraqis in the previous match.
"I am a midfielder and as a No 6 I felt most comfortable out there tonight," Milligan said post match.
"But I want to win, no matter who we play. We were a bit soft in certain areas the other day.
"I don't think any Australian likes being looked in the face and told they're a bit soft so we made sure we turned that around and I made it my job to lead from the front."
Postecoglou was magnanimous in his praise for his dependable warrior, who at the age of 20 was a member of Australia's 2006 World Cup squad.
The two worked together at club level at Melbourne Victory before the coach was enticed by the national job three and a half years ago. Milligan now plays for Baniyas in the UAE's Pro League.
"We always knew that their major threat was going to be in transition if we gave the ball away," Postecoglou said.
"They have dangerous players that can hurt you but Millsy and Mile did a terrific job in nullifying that.
"On the ball Millsy is very brave. He asked for it in tight areas and kept things ticking along."
The Australians' victory was thoroughly deserved although it was only in the second half that the team hit its stride.
After scoring early with a heavily deflected header from the impressive Jackson Irvine, cheap turnovers became the order of the day but the team's overall performance improved after the break, thanks largely to the forceful runs on either wing from Mathew Leckie and Brad Smith that stretched the visitors.
It certainly was no collective masterpiece - far from it - but sometimes results are far more important than the manner in which they are achieved and you could sense the relief of the 27,328 crowd when Leckie scored the second goal that finally broke the UAE's resistance and effectively sealed the outcome.
This key qualifier was one such match.
The Socceroos' next game is against joint group leaders Saudi Arabia in Adelaide in June.