Genia comes in for Nic White in the only change to the starting line-up from that beaten 28-8 by South Africa in Cape Town last weekend.
White drops to the bench for the wooden-spoon showdown at Estadio Gigante de Arroyito in Rosario, 300 kilometres north west of Buenos Aires.
There is also one change among the replacements with utility back Bernard Foley coming in for Chris Feauai-Sautia, scorer of the Wallaby try against the Springboks.
Papua New Guinea-born Genia, 25, has skippered Australia this year in the absence of injured lock James Horwill.
But he was axed by coach Ewen McKenzie after leading the Wallabies in a humiliating 26-point drubbing by South Africa in Brisbane.
White impressed sufficiently to stay on the pitch for the full 80 minutes as Australia squeezed a 14-13 home win over the Pumas in a dour duel.
But his field-kicking came unstuck in Cape Town and the Wallabies fared far better when Genia came on for the second half.
McKenzie, a Super Rugby title-winning coach with the Reds, replaced New Zealander Robbie Deans after a 2-1 series loss to the British and Irish Lions.
But the former Wallaby prop has experienced a baptism of fire with home and away reverses against the New Zealand All Blacks and the Springboks.
Since arriving in Argentina, McKenzie admitted that trying to slug it out with South Africa in a field-kicking contest was a blunder.
He emphasised to his squad the need to play it off the cuff at times, with natural runner and full-back Israel Folau expected to keep the ball in hand more.
Australia have four points and Argentina two after five rounds, meaning the losers of the final 2013 Rugby Championship fixture get the unwanted wooden spoon.
The Wallabies have a slight advantage in previous meeting on Argentine soil with four victories, three losses and one draw.
15 Juan Martin Hernandez, 14 Horacio Agulla, 13 Marcelo Bosch, 12 Felipe Contepomi, 11 Juan Imhoff, 10 Nicolas Sanchez, 9 Martin Landajo, 8 Juan Manuel Leguizamon, 7 Pablo Matera, 6 Juan Fernandez Lobbe (captain), 5 Patricio Albacete, 4 Julio Farias Cabello, 3 Juan Figallo, 2 Eusebio Guinazu, 1 Marcos Ayerza
Substitutes: 16-Agustin Creevy, 17-Nahuel Lobo, 18-Juan Pablo Orlandi, 19-Manuel Carizza, 20-Benjamín Macome, 21-Tomas Cubelli, 22-Santiago Fernandez, 23-Lucas Gonzalez Amorosino
15 Israel Folau, 14 Adam Ashley-Cooper, 13 Tevita Kuridrani, 12 Christian Leali’ifano, 11 Joe Tomane, 10 Quade Cooper, 9 Will Genia, 8 Ben Mowen, 7 Michael Hooper, 6 Scott Fardy, 5 Rob Simmons, 4 James Horwill (captain), 3 Ben Alexander, 2 Stephen Moore, 1 James Slipper
Substitutes: 16 Saia Faingaa, 17 Benn Robinson, 18 Sekope Kepu, 19 Sitaleki Timani, 20 Ben McCalman, 21 Nic White, 22 Matt Toomua, 23 Bernard Foley