O'Mahony's move to the number seven jersey has allowed Schmidt to bring in Leinster number eight Jack Conan and switch CJ Stander to the blindside of the scrum, giving the visitors a big, combative loose forward trio for the Sydney test on Saturday.
Schmidt also shook up his front row with loosehead prop Jack McGrath coming back into the starting side with Cian Healy dropping to the bench, while Sean Cronin will start at hooker.
Niall Scannell, who started last week's 26-21 victory, is the replacement hooker.
Winger Jacob Stockdale, who started the first test, has also returned to the side with Keith Earls shifting to the right wing to accommodate the 22-year-old from Ulster.
Andrew Conway has dropped out of the 23-man match day squad altogether.
Bundee Aki returns at inside centre with Robbie Henshaw shifting out to centre and Garry Ringrose dropping out of the squad.
Leinster flyhalf Joey Carbery, who started the first test in Brisbane but was replaced by Johnny Sexton for the second, has also dropped out of the matchday squad with Ross Byrne deputising off the bench for Sexton.
Team: 15-Rob Kearney, 14-Keith Earls, 13-Robbie Henshaw, 12-Bundee Aki, 11-Jacob Stockdale, 10-Johnny Sexton, 9-Conor Murray, 8-Jack Conan, 7-Peter O'Mahony (captain), 6-CJ Stander, 5-James Ryan, 4-Devin Toner, 3-Tadhg Furlong, 2-Sean Cronin, 1-Jack McGrath.
Replacements: 16-Niall Scannell, 17-Cian Healy, 18-John Ryan, 19-Tadhg Beirne, 20-Jordi Murphy, 21-Kieran Marmion, 22-Ross Byrne, 23-Jordan Larmour.
(Reporting by Greg Stutchbury in Wellington; Editing by Peter Rutherford)
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