Arsenal were the dominant team from the opening minutes but were unable to unlock a stubborn All Stars defence until England striker Alessia Russo nodded home in the 39th minute in front of 42,120 fans.
Cooney-Cross sent some nerves through Marvel Stadium when she went down in the 72nd minute holding her right calf, seemingly with cramp, after a clip from Melbourne City and All Stars forward Rhianna Pollicina.
The Matildas gun was jovial on the ground, refused to come off on a stretcher and was in good spirits as she left the pitch.
Cooney-Cross is among the Matildas taking part in two friendlies against China on May 31 and June 3.
Australia's Kyra Cooney-Cross was a danger for Arsenal, despite a minor injury scare. (James Ross/AAP PHOTOS)
Arsenal coach Jonas Eidevall fielded a strong starting line-up, with Foord, Cooney-Cross, Catley, captain Kim Little, Ireland skipper Katie McCabe and Russo among their starters.
All Stars counterpart Joe Montemurro opted for experience, with seven capped Matildas among his starting XI, including Cortnee Vine, Michelle Heyman and Tameka Yallop.
But Arsenal's quality shone through from the opening minutes as the Gunners dominated possession and controlled the midfield, while Foord had her various markers on skates.
But it took a 17-year-old to unlock a hard-working defence marshalled by New Zealand international Rebekah Stott and Melbourne Victory skipper Kayla Morrison.
Teenager Vivienne Lia dipped a wonderful ball into the box and Russo, who had made a terrific ghosting run between Rebekah Stott and Alana Cerne made no mistake, leaping high to nod the ball home.
The Matildas' Caitlin Foord was her usual attacking self for Arsenal. (Joel Carrett/AAP PHOTOS)
Retiring Matildas great and former Arsenal goalkeeper Williams was substituted for Jada Whyman just before half-time, receiving a rousing ovation from the crowd and plenty of love from players on both sides.
The All Stars were able to create several half-chances but without reward.
Foord forced a save from Jada Whyman in the 79th minute and made way four minutes later, to a raucous reception from the home fans.
The All Stars could have equalised at the death when Mackenzie Hawkesby slipped through Hannah Wilkinson, but the New Zealand international was denied by an excellent save from Naomi WIlliams.
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