The injury cast a huge shadow over Gareth Jenkins' tourists as they flew home in the knowledge the five-times capped Cardiff Blue will miss the World Cup and 2008 RBS Six Nations Championship.
Czekaj suffered the injury in the 22nd minute, twisting badly as he tried to offload in a tackle by Wallaby hooker Stephen Moore.
The 21-year-old underwent surgery today in Brisbane as the tour party headed for the airport and the Welsh Rugby Union are flying his girlfriend out to be with the 6ft 3in player who has been told he cannot fly home for at least 14 days after the operation.
However, despite the defeat and the fact Wales were largely on defensive duties during their defeats in both Tests, coach Jenkins hinted veteran Colin Charvis and 2005 Grand Slam skipper Michael Owen are among those to have done their chances of appearing at the autumn tournament a power of good.
Charvis was Wales' outstanding performer in Sydney and Brisbane, overcoming the difficulties of a lack of possession from the front five on each occasion to outplay world class-rated Phil Waugh and George Smith.
Owen replaced Brent Cockbain in the first Test and in the Australian-born player's absence through injury, impressed around the field with some fine footballing touches.
Jenkins said: "There are no complaints. It wasn't even close and full credit to Australia. But Charvis has proven to everybody here at 34 that he still has world class in him and he was great. Michael Owen brought a lot of continuity as a ball-carrier.
"I'm pleased with the performances of the likes of Colin and other experienced players.
"This tour has allowed players like Colin and Michael, who didn't have the opportunity in the Six Nations, to make a statement and they did it in great style and fashion.
"They both have an appetite to wear the jersey and want to be part of the World Cup squad and they played like that.
"This tour has given me the type of problems any coach wants - strength in depth with competitive players who all have ambition - and players with quality too. It's given me a headache I'm grateful for."
Jenkins was also relieved to see Gavin Henson back in action after a second successive season the Osprey would rather forget while James Hook continued to show flashes of the brilliance that have turned him from a semi-professional with Neath into one of the game's hottest properties.
"It was a big plus for us to get Gavin on the field and getting him into the rugby and I felt he needed that.
"That's a plus, and James Hook has played one and a half games at 10 which is good for his development as well."
Skipper Gareth Thomas also earned the coach's seal of approval with Jenkins saying: "Gareth Thomas is still figuring in the captaincy role and the general way he manages a group of players."
Thomas said: "Possession was a big problem. If you want to play attacking rugby and you're defending all the time, you can't do that.
"But we have to give some credit to Australia too. They strangled the ball and kept it away from us and we can't do anything about that.
"It was 6-0 at half-time, but Australia probably went into the second period the more confident team. We defended bravely and admirably up until then and thought the break would be good for us.
"We came out ready to play in the second half, but Australia got the ball and scored a try and they were gone and strangled the ball again."