Wales responded through a driving maul with Lake powering over and Thomas converting before Lolesio kicked a second penalty.
Wales lost prop Archie Griffin to a head injury assessment after he was the victim of a shoulder to the head by Australia lock Lukhan Salakaia-Loto, who was shown a yellow card.
Lake turned down a kick at goal to go for the corner to attempt to score a try and he was rewarded for his bravery with Thomas converting.
A huge Valetini tackle forced a penalty which Lolesio was successful with to give Australia a nine-point half-time lead.
With Griffin returning to the field, Wales rallied after the break with some patient build-up before wing Williams crossed in the opposite corner with Thomas' conversion reducing the deficit to two points.
More Wales indiscipline relieved pressure and replacement prop Alaalatoa crossed for his first Test try.
Daugunu was gifted a second score after Williams tried to keep the ball in play, only to guide possession into the hands of the advancing Australia wing.
Wing Dyer produced a sensational finish to bring Wales back into the game and their hopes improved thanks to Sam Costelow's touchline conversion.
Wales had another attacking chance, but their line-out failed them at a crucial time with replacement hooker Evan Lloyd failing to find Cory Hill.
Australia's Ben Donaldson kicked a late penalty to ensure it was Slipper lifting the James Bevan Trophy.
Australia: T Wright; Kellaway, Flook, Paisami, Daugunu; Lolesio, J Gordon; Slipper (capt), M Faessler, Tupou, J Williams, Salakaia-Loto, Valetini, McReight, Cale.
Replacements: Nasser, Kailea, Alaalatoa, Blyth, Gleeson, White, Donaldson, Pietsch.
Sin-bin: Salakaia-Loto 35
Wales: Winnett; L Williams, Watkin, Grady, Dyer; B Thomas, Bevan; G Thomas, Lake (capt), Griffin, Tshiunza, D Jenkins, Botham, Reffell, Plumtree.
Replacements: E Lloyd, Mathias, H O'Connor, Hill, Martin, Hardy, Costelow, Tompkins.
Referee: Nika Amashukeli (GRU)
Assistant referees: Matthew Carley (RFU), Paul Williams (NZR)
TMO: Glenn Newman (NZR).