In a team captained by David Pocock, Toomua has replaced Christian Lealiifano, who played the full 80 minutes against Uruguay but is back on the bench under a workload management approach from Wallabies coaches.
Nic White remains the starting scrum-half.
Wallabies coach Michael Cheika said Toomua's impressive stints off the bench in the opening two matches had earned him a chance to start in the chief playmaking spot.
"He's filled in there and done quite well there," he said. "He's a different player to Lealiifano and Foley. He's got a different style and a different type of defender and he's done well in the opportunities he's been given.
"Admittedly they've been second halves, where we've had more of a direct line and we want to try and start like that.
"We're giving him an opportunity to show his wares and with Christian on the bench, they'll be working in tandem just in a different order."
This is the third week in a row that the Wallabies have reshuffled their side and the third different halves partnership, something Cheika said was about ensuring players stayed on their toes.
"This is how we think this squad's best is to keep giving opportunities to guys to keep the contest alive with others so if we do the right thing and get through knockout stages, we know everyone's been a part of doing their bit," he added.
In a much-changed starting line-up from their clash with Uruguay, Jordan Petaia will run on for his second Test cap in Shizuoka after impressing against Los Teros in Oita, and with Marika Koroibete returning from a week off, Dane Haylett-Petty returns to the bench at the expense of Adam Ashley-Cooper.
Up front, Pocock will skipper the team from openside flanker, with regular captain Michael Hooper switching roles from last week and being named on the bench.
It is the first time Hooper has been named on the bench since a game against Argentina in Mendoza in 2015, but like Pocock in Oita, he is expected to get 30 minutes at the end of the game.
Jack Dempsey will start at blindside flanker and Isi Naisarani returns at number eight.
Allan Alaalatoa has been rested in the front-row and will be replaced by Sekope Kepu, with Taniela Tupou still on the bench.
Hooker Tolu Latu and Scott Sio also return in the front-row.
Starting locks Izack Rodda and Rory Arnold both resume their spots in the starting side after not playing against Uruguay last week.
Despite a storming game last week against Uruguay, Tevita Kuridrani was left out of the 23.
Samu Kerevi and James O'Connor will both return to the starting midfield and Haylett-Petty's versatility was preferred on the bench.
Cheika said another round of changes was part of the strategy they wanted to follow in the World Cup, keen to keep players on their toes.
"Different teams do it differently," he said. "Some want to go with the same players all the time and rest out.
"We feel like keeping players competing for spots is working for us, I think we're playing some good footy. This is another chance for other guys to do the same."
The Wallabies' clash with Georgia will be the first between the two nations in Test rugby and Cheika said it would be an exciting moment for the countries.
"They're very physical, that's quite obvious, it'll be a really good challenge for us," he said. "A lot of players play in professional leagues in France, England as well, they're well attuned to competition at a high level.
"It's really exciting to be part of the first time two countries have ever faced off. We want to show them how we play our rugby and I'm sure they'll be showing us how they play theirs."
Australia: 15 Kurtley Beale, 14 Jordan Petaia, 13 James O'Connor, 12 Samu Kerevi, 11 Marika Koroibete, 10 Matt Toomua, 9 Nic White, 8 Isi Naisarani, 7 David Pocock (c), 6 Jack Dempsey, 5 Rory Arnold, 4 Izack Rodda, 3 Sekope Kepu, 2 Tolu Latu, 1 Scott Sio
Replacements: 16 Jordan Uelese, 17 James Slipper, 18 Taniela Tupou, 19 Adam Coleman, 20 Michael Hooper, 21 Will Genia, 22 Christian Lealiifano, 23 Dane Haylett-Petty
Date: Friday, October 11
Venue: Shizuoka Stadium Ecopa
Kick-off: 19:.45 local (11:45 BST, 10:45 GMT)
Referee: Pascal Gauzere (France)
Assistant referees: Jérôme Garcès (France), Shuhei Kubo (Japan)
TMO: Marius Jonker (South Africa)