Cronin started last month's match in Rome but struggled at the line-out and failed to make the case that he could replace usual starter Rory Best.
Head coach Joe Schmidt gave British and Irish Lions star Henshaw, who missed out against Scotland and Italy after failing to shake off a dead leg, every chance to prove his fitness but he has not recovered in time.
Flyhalf Joey Carbery is included in the squad for Sunday's match after a hamstring injury together with halfbacks Ross Byrne and Kieran Marmion.
Rob Herring is picked as one of three hookers alongside skipper Best and Munster's Niall Scannell.
Forwards coach Simon Easterby rejected the notion that Cronin, who was making his first-ever Six Nations start while earning his 68th cap against Italy, had been treated harshly and said his exclusion would not hurt his World Cup hopes.
"It's to do with building some depth and we know a lot about Sean," he said.
"He has been in camp a long time, he has been in the squad a long time and has a lot of caps.
"It's an opportunity to see a bit more of other players. That doesn't exclude him from next week and it certainly doesn't exclude him from us going forward."
Easterby said Carbery trained on Wednesday but was unlikely to feature against France and suggested it was touch and go whether injured pair Henshaw and Dan Leavy would be back to face Wales in their final Six Nations match on March 16.
"It's about making sure they're right and ready to play and not compromising their return," he said.
"It may well be that they don't feature but we will assess that as we go along this week and then with the short turnaround the week after, it would be great if we could have some fresh bodies coming back in, but it might be too soon for both of them."
Ireland, who won the Grand Slam last year, are third in the Six Nations table with two wins from their opening three games.