Kearney was omitted from the 31-man squad announced by coach Declan Kidney on Wednesday after being told he requires surgery.
The reigning European player of the year is expected to be out for eight to 10 weeks.
Earlier this week Kearney had declared himself fit for next month's Tests against South Africa, Fiji and Argentina, but a specialist has since advised surgery, which the Leinster man will undergo on Thursday.
The 26-year-old had played just 32 minutes of rugby this season because of the back problem, but had hoped to return to action this weekend.
His absence leaves Ireland short on options to fill the number 15 jersey with Luke Fitzgerald and Gavin Duffy injured, Felix Jones left out of the 31 after recently returning from a spell in the treatment room and Geordan Murphy having retired from Test rugby.
Munster's Keith Earls is the most obvious choice to replace Kearney, although he is currently out with a groin problem, while Tommy Bowe is also an option.
Flanker Stephen Ferris and fly-half Ronan O'Gara feature among the 31 despite their recent struggle with respective back and hamstring injuries.
Centre Luke Marshall, back-rower Iain Henderson, prop David Kilcoyne and hooker Richardt Strauss are the four uncapped players included.
Strauss, born and raised in South Africa but uncapped by the Springboks, qualifies for Ireland on residency grounds this month having represented Leinster since 2009.
It was also announced that Munster assistant coach Anthony Foley has been added to Ireland's backroom team as part of a reshuffle.
Foley will oversee the defence, allowing Les Kiss to become attack and backs coach.
Kidney said: "We have three incredibly competitive games ahead of us and while there have been quite a few injuries and niggles in the early part of the season, it has opened up opportunities for other players.
"There are world ranking points on offer, so the underlying challenge for us is to work towards retaining and improving our ranking position ahead of the World Cup pool draw.
"While that is the end goal, our focus will be getting our preparations right to match the intensity of international games.
"I'm pleased that Anthony has taken up the offer of working with the squad to assist during this vital period in November.
"His previous experience of working with the team during the last RBS 6 Nations championship was important, but his own abilities and experience were central to bringing him on board."
Ireland squad for 2012 Guinness Series games against South Africa, Fiji and Argentina:
Backs: T Bowe (Ulster), D Cave (Ulster), G D'Arcy (Leinster), K Earls (Munster), L Marshall (Ulster), F McFadden (Leinster), C Murray (Munster), B O'Driscoll (Leinster, capt), R O'Gara (Munster), E Reddan (Leinster), J Sexton (Leinster), A Trimble (Ulster), S Zebo (Munster).
Forwards: R Best (Ulster), T Court (Ulster), S Ferris (Ulster), C Healy (Leinster), J Heaslip (Leinster), I Henderson (Ulster), C Henry (Ulster), D Kilcoyne (Munster), M McCarthy (Connacht), K McLaughlin (Leinster), J Muldoon (Connacht), D O'Callaghan (Munster), P O'Connell (Munster), P O'Mahony (Munster), M Ross (Leinster), D Ryan (Munster), R Strauss (Leinster), D Tuohy (Ulster).
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