Robin McBryde's side won the first test 22-18 in Osaka last weekend and will be looking for their sixth consecutive victory on Saturday.
The only change in the front row sees Saracens prop Gill come into the side alongside Emyr Phillips (Scarlets), who will win his second cap and Blues prop Scott Andrews.
Captain Bradley Davies (Blues) continues his partnership with regional teammate Lou Reed in the second row.
The new look back row sees James King (Ospreys) switch to blindside, Navidi comes in at openside flanker and Andries Pretorius (Blues), starts for the first time for Wales at number eight.
There is just one change behind the backline where Prydie comes onto the wing.
Lloyd Williams (Blues) and Dan Biggar (Ospreys) continue at half-back with Jonathan Spratt (Ospreys) and Owen Williams (Blues) again linking up in the centre.
Liam Williams (Scarlets) and try-scorer in Osaka Harry Robinson (Blues), line-up in the back three alongside Prydie.
Ospreys hooker Scott Baldwin and Scarlets prop Rhodri Jones are again named amongst the replacements. They are joined by Craig Mitchell (Exeter Chiefs) and Dragons' Andrew Coombs. Dan Baker (Ospreys) who made in debut last weekend again features on the bench alongside Tavis Knoyle (Scarlets), Rhys Patchell (Blues) and Dafydd Howells (Ospreys).
"We were proud of the side's effort last weekend but know we will have to step it up again on Saturday," said Head Coach for the Japan tour Robin McBryde.
"It was good to see the character of the squad come through in the first test and we will need that again.
"The players have again all put their hands up for selection making it a tough call for us and that shows their determination to get out on the field and represent their country.
"Japan showed what they are capable of last weekend and we know we will have to be at our best to get the second victory and finish the season on a high."
Liam Williams (Scarlets), Harry Robinson (Blues), Owen Williams (Blues), Jonathan Spratt (Ospreys), Tom Prydie (Dragons), Dan Biggar (Ospreys), Lloyd Williams (Blues), Rhys Gill (Saracens), Emyr Phillips (Scarlets), Scott Andrews (Blues), Bradley Davies (CAPT) (Blues), Lou Reed (Blues), James King (Ospreys), Josh Navidi (Blues), Andries Pretorius (Blues).
Replacements: Scott Baldwin (Ospreys), Rhodri Jones (Scarlets), Craig Mitchell (Exeter Chiefs), Andrew Coombs (Dragons), Dan Baker (Ospreys), Tavis Knoyle (Scarlets), Rhys Patchell (Blues), Dafydd Howells (Ospreys).