Sexton injured his shoulder during Leinster's Pro 12 final defeat to Connacht on Saturday and underwent minor surgery this week. Fitzgerald and Dave Kearney picked up injuries in the same game while his brother, Rob, strained his hamstring in training.
Sexton is expected to return to action at the start of next season, the IRFU said.
Bordeaux-bound Ian Madigan was called up to replace the British and Irish Lions' flyhalf. Ulster winger Craig Gilroy also returns to the squad along with the uncapped Connacht duo of fullback Tiernan O'Halloran and wing Matt Healy.
Healy, 27, was particularly unlucky not to have made the original squad having finished joint top try scorer with Gilroy in the Pro12, including a try in Saturday's defeat of Leinster that handed Connacht an unlikely first league tile.
Ireland, who failed to capture an unprecedented third Six Nations in a row earlier this year, were already without Cian Healy, Josh van der Flier, Peter O'Mahony, Sean O'Brien, Tommy Bowe and Simon Zebo for the tour.
Joe Schmidt's men face the Springboks in Cape Town on June 11 before travelling to Johannesburg a week later and finishing in Port Elizabeth on June 25.
(Reporting by Padraic Halpin; Editing by Jon Boyle)
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