The Connacht fly-half gets the nod after Sexton missed training early in the week with a quad injury.
As well as Carty, the other three changes come in the backline where Chris Farrell comes in for Bundee Aki, while in the back three Rob Kearney and Keith Earls have both recovered from niggles to take their place in the side.
That means that Jordan Larmour drops down to the bench, while Andrew Conway misses out on the matchday 23 altogether.
Rory Best captains the team once again in an unchanged pack, with Peter O’Mahony having come through the HIA protocols to feature.
On the bench Jack Conan misses out having picked up a niggle in training, meaning that Rhys Ruddock is named among the replacements.
The match in Shizuoka on Saturday pits two sides with maximum points from their opening game against one another.
Japan saw off Russia on the opening night in Tokyo, while Ireland beat Scotland in Yokohama on Sunday.
Ireland team to face Japan:
15. Rob Kearney (Leinster)
14. Keith Earls (Munster)
13. Garry Ringrose (Leinster)
12. Chris Farrell (Munster)
11. Jacob Stockdale (Ulster)
10. Jack Carty (Connacht)
9. Conor Murray (Munster)
1. Cian Healy (Leinster)
2. Rory Best (Ulster) (c)
3. Tadhg Furlong (Leinster)
4. Iain Henderson (Ulster)
5. James Ryan (Leinster)
6. Peter O’Mahony (Munster)
7. Josh van der Flier (Leinster)
8. CJ Stander (Munster)
Replacements
16. Sean Cronin (Leinster)
17. Dave Kilcoyne (Munster)
18. Andrew Porter (Leinster)
19. Tadhg Beirne (Munster)
20. Rhys Ruddock (Leinster)
21. Luke McGrath (Leinster)
22. Joey Carbery (Munster)
23. Jordan Larmour (Leinster)
