Doubles from Panagiotis Nikas, David Zdrilic and Peter Crevani saw the Beach Socceroos end their group campaign with three wins.
Australia sailed through to the semi-finals where it will take on Japan while United Arab Emirates and Iran clash in the other final four meeting.
The top three sides qualify for September's Beach Soccer World Cup.
Australia went into the clash against Afghanistan in the knowledge that only a win would ensure its progress from the group stage, and it had to make do without George Souris and Ante Juric. The tough schedule taking its toll on the veteran defenders.
With both sides desperate for victory at Katara Beach, the game wasted little time in heating up.
Afghanistan went ahead after just three minutes through Samiullah Mohammadi. His free kick from range curled into the top right hand corner to give Aussie keeper Simon Jaeger no chance.
Within a minute Australia equalised when Zdrilic's cross from the right found the heaad of an unmarked Nikas at the far post and he couldn't miss the wide open goal.
Australia had the better of the first period with Zdrilic and Nikas lively up front and they tested Afghan goalkeeper Mujtaba Haidari on numerous occasions.
In the second period Nikas wasted little time in restoring Australia's lead when he was awarded a free kick and then duly converted with a shot into the left hand corner of the goal. It was his eighth goal of the tournament.
But the advantage lasted less than 30 seconds. Mahmood Azad converted a penalty when his spot kick sent Jaeger the wrong way and nestled into the net.
Two quick-fire goals then swung the momentum back Australia's way. Zdrilic received a Michael Matricciani ball with his right foot, swivellied and fired a left-foot shot from close range past a helpless Haidari.
Crevani opened his account for the match with a side-footed free kick that deceived Haidari in its simplicity as the Beach Socceroos went into the final third of the game leading 4-2.
The margin was extended a minute into the final period as Crevani netted another free kick. This spectacular effort from a long way out sailed into the goal.
Before Australia could start thinking about cruising to victory, Afghanistan hit back quickly and decisively.
The combination of a long and direct Haidari throw out and a flick-on header from Mohammadi worked to perfection twice in the matter of seconds to reduce the deficit to a single goal.
But a touch of brilliance from Zdrilic with a matter of minutes remaining rounded off the scoring and put to bed the outcome.
After he won a corner, his low drive with the outside of his right foot flew into the net past an unsuspecting Haidari.
The three points secured the group win for Australia, which has two bites at the cherry to qualify for the Beach Soccer World Cup in Tahiti.
Beach Socceroos coach Airton Andrioli was ecstatic with his team's win.
"We couldn’t have asked for any better," he said.
"When we came here nobody expected anything like this, so credit to the boys, they did a fantastic job.
"We’re looking forward to going one step further in the next match. We’re going to continue to fight and we’ll see what happens at the end. But the boys have done extremely well, I’m really proud of them."