Henry tore his hamstring during the comprehensive 40-9 victory by Joe Schmidt's men and is now expected to be out of action for at least four weeks, maybe even six.
"Unfortunately, Chris suffered a hamstring tear on Saturday and will miss the rest of the series, so Shane Jennings has been called in as a replacement," Ireland team manager Michael Kearney said.
Meanwhile, Tommy Bowe suffered bruising to his leg against Samoa and has at least been ruled out of training, with Luke Fitzgerald called in to cover.
But the side are hoping that Bowe will be fit to face Australia in Dublin on Saturday.
"With Tommy, it's really a day-to-day thing," Kearney added.
"So it's got to be day-to-day as we monitor his progress."
Centre Keith Earls continues to battle his knee trouble and is also being monitored, but Brian O'Driscoll, Paul O'Connell and Sean O'Brien have all recovered well from their recent injuries.