Sexton, 30, had been named in the starting lineup despite limping off the field in last weekend's pool win over France but felt some discomfort after training on Friday.
The Irish playmaker was sent for scans which revealed he had a minor abductor strain, prompting team officials to withdraw him from the match and replace him with Ian Madigan.
"He was pretty down on himself after last week, having to come off and he did everything he could this week," Ireland forwards coach Simon Easterby told a news conference on Saturday.
"He trained yesterday and unfortunately it's one of those things, in his position as well, having to kick the ball as much as he does and be very accurate.
"It just meant that it wasn't quite right and we weren't prepared to take that risk going into such a big game."
Scrumhalf Isaac Boss has been brought in to the squad as extra cover for the injured Jared Payne as Madigan had also been the back-up scrum-half behind Conor Murray and Eoin Reddan.
Madigan, 26, has served as Sexton's understudy in the Ireland team since 2013 but made a big impression when he came on against France, kicking two penalties and a conversion.
"Mads showed real quality last weekend to step into a really pressurised situation and come through very strongly and we were probably fortunate it was an easy switch over," Easterby said.
"Mads is a confident guy, he's kicking extremely well at the moment, he's striking the ball really well of the tee and he's one of these guys who will really thrive in this environment."
LATEST SETBACK
The loss of Sexton is the latest setback for a bruised and battered Ireland team bidding to reach the World Cup semi-finals for the first time.
Captain Paul O'Connell and blindside flanker Peter O'Mahony were both replaced in the squad after suffering injuries against France, while openside flanker Sean O'Brien received a one-week ban for punching.
"They're all guys you'd like to have in your squad but that's the nature of the game," Ireland's stand-in skipper Jamie Heaslip said.
"Guys get banged up and you just gotta play with the hand you're dealt with.
Heaslip said Sexton's late withdrawal would not alter the way Ireland approached the match against the Pumas because everyone in the squad was ready to step in at any stage.
"It doesn't change the game plan at all. I think you saw last week when Johnny came off after 20-25 minutes, Ian stepped in and we all get the same game plan that we've run through during the week," Heaslip said.
"We never talk about individuals as such, but we talk about the strength individuals can bring to the group. Granted, Johnny is probably one of the best out-halves out there, but playing with Ian for the last couple of years he’s no slouch either.”
(Editing by Ed Osmond)
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