The Socceroos, playing their 500th international match, were expected to make amends for a dour 0-0 draw with the United Arab Emirates on Friday when they took to the field in Doha.
However, although Tuesday's contest at the Abdullah bin Nasser bin Khalifa Stadium proved a more entertaining affair, the men in green and gold again proved unable to breach the opposition's defence, and also conceded a soft goal.
Khalfan struck in the 61st minute, springing an offside trap to latch on to a pass from Sebastian Soria and slot a low finish beyond Adam Federici.
Australia coach Ange Postecoglou made eight changes to the starting XI held by the UAE, with centre-back Alex Wilkinson, captain Mile Jedinak and forward Robbie Kruse the only survivors.
It took just two minutes for some familiar faces to resume a well-established partnership. Mark Bresciano picked out Tim Cahill unmarked at the back post, only for the New York Red Bulls man to send an uncharacteristically weak effort harmlessly into the turf.
Despite dominating possession, the Socceroos had to wait until the 24th minute for another presentable chance to arrive. This time Cahill, winning an aerial challenge inside the area, nodded down to James Troisi, who saw the angle for a right-footed curler closed off, before his eventual left-footed strike was well saved by goalkeeper Qasem Burhan.
Australia, who introduced Federici and Josh Brillante for Mitch Langerak and Jedinak at half-time, stepped things up early in the second half, although a succession of corners and half-chances failed to really trouble the hosts.
Qatar then took advantage of their opponents' wastefulness as Khalfan opened the scoring.
Cahill had a decent chance to level in the 68th minute, turning his man just inside the area before firing a low strike straight at Qasem.
However, Australia were unable to recapture the momentum they had built earlier in the second period as Qatar held out with relative comfort.
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