Huddersfield tested the Arsenal defence through most of the match with Mooy playing a major part.
With Mooy pulling the strings in midfield the Terriers created their fair share of chances but were let down by terrible finishing in front of goal.
It was costly for Huddersfield as goals to Arsenal's Alexandre Lacazette and Alex Iwobi gave the Gunners a 2-0 advantage at the break.
With the game deep in injury time, Mooy unleashed a cutting through ball to create Huddersfield's only goal of the game.
It is only Mooy's third game back since the serious knee injury which sidelined him for Australia's Asian Cup title defence.
The result left Huddersfield anchored to the bottom of the Premier League and 13 points below safety in the relegation zone.
Another Socceroos star in action was Mat Ryan who had a disappointing showing for Brighton and Hove Albion in their 3-1 loss against Burnley.
Burnley's Kiwi striker Chris Wood had the better of Ryan for most of the game as he claimed a brace in the win.
Brighton claimed a late goal but it proved to be a mere consolation after a poor performance from the Seagulls.
Results weren't going the way of Australia's players in the Championship either.
Massimo Luongo clocked a full 90 minutes for QPR but was unable to guide his side to victory as they suffered a 4-3 defeat to Birmingham City.
It was a similar story for Jackson Irvine who started and played the whole match in Hull City's 2-0 loss to Derby County.
Bailey Wright shook the trend as he helped his Bristol City side to a narrow 1-0 win against Blackburn Rovers.
Wright started the match but was substituted in the 63rd minute for Eros Pisano who went on to score the match winner.
In League One, Kenneth Dougall continues his comeback from injury as he came off the bench in Barnsley's 4-1 win against Gillingham, as did Bradden Inman in Rochedale's 1-0 loss at Coventry City.
Cameron Burgess played 90 minutes in Scunthorpe's 2-0 win.
In Germany Robbie Kruse was given a full shift for second division side Bochum as they lost 2-1 to Paderborn.
In Scotland Mark Milligan started for Hibernian as they claimed a 3-1 win in the Scottish FA Cup against Raith Rovers.
The Socceroos captain was substituted after 79 minutes.
Danny Vukovic's Belgian side Genk continued their domination of the Belgian Pro League by stretching their advantage at the top of the table with a 2-0 win against Standard Liege.
Vukovic was in fine form to keep a clean sheet in the win.
Mustafa Amini was also on a winning team as his Danish side Aarhus defeated Esbjerg 2-0 to keep in the running for European qualification.
Finally, Australian midfielders Erik Paartalu and Chris Herd faced off in the Indian Super League overnight.
Herd's Chennaiyin side taking home the points after a 2-1 triumph over Paartalu's Bengaluru.
