O'Brien trained fully this week after recovering from a calf injury and joins Jamie Heaslip and CJ Stander in the same back row that started Ireland's bruising loss to New Zealand in Dublin last November.
British and Irish Lions flyhalf Sexton, who has struggled for fitness all season, was ruled out of the opener in Edinburgh earlier this week after complaining of tightness in his injured calf, joining centre Jared Payne on the sidelines.
Paddy Jackson take Sexton's place at number 10 while Schmidt has plenty of options at centre, opting to start the exciting young Leinster combination of Robbie Henshaw and Garry Ringrose.
"I'd say realistically Johnny is an outside chance for Italy (on Feb. 11). He's probably played about 82 minutes for the national team in the last eight test matches, so for us it is a real frustration," Schmidt told a news conference on Thursday.
"In the three Six Nations I have been involved in, Johnny has dominated the number 10 position so we're still hopeful that he can come back in and do that for us. At the same time, Paddy has trained really well and it's not like he hasn't had some really good experience in recent times at a very high level."
Elsewhere combative Ulster lock Iain Henderson starts beside Devin Toner in the second row after Donnacha Ryan, a key part of the successful November series when Ireland beat the All Blacks in Chicago and Australia, was not risked after returning to training this week from a niggling medial ligament injury.
Schmidt said he was pretty confident winger Andrew Trimble would be fit for next week's game in Rome but flanker Peter O'Mahony was highly unlikely to feature with a hamstring strain.
Ireland team: 15-Rob Kearney, 14-Keith Earls, 13-Robbie Henshaw, 12-Garry Ringrose, 11-Simon Zebo, 10-Paddy Jackson, 9-Conor Murray; 8-Jamie Heaslip, 7-Sean O'Brien, 6-CJ Stander, 5-Devin Toner, 4-Iain Henderson, 3-Tadhg Furlong, 2-Rory Best (captain), 1-Jack McGrath
Replacements: 16-Niall Scannell, 17-Cian Healy, 18-John Ryan, 19-Ultan Dillane, 20-Josh van der Flier, 21-Kieran Marmion, 22-Ian Keatley, 23-Tommy Bowe.
(Reporting by Padraic Halpin, editing by Pritha Sarkar)
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