Varney went off injured in the loss to Ireland on August 5th but was included in Italy's final World Cup squad.
Varney takes over from Alessandro Garbisi and outside back Paolo Odogwu drops to the bench after scoring a try in the 57-7 win over Romania on Saturday.
Tommaso Allan makes his return to the number 15 jersey after sitting out the Romania game. Winger Ange Capuozzo made an impressive comeback from injury to score two tries in that game and starts against Japan.
"The game against Japan will close the preparations for the World Cup by giving us further fundamental feedback towards the most important moment of the season," coach Kieran Crowley said.
"We have prepared the game in the best possible way and we want to close the warm-up games with a victory in front of our fans."
Italy play Japan on Saturday in Treviso.
In World Cup Pool A, they will meet hosts France, three-time world champions New Zealand, Namibia and Uruguay.
Italy team:
15-Tommaso Allan 14-Ange Capuozzo 13-Juan Ignacio Brex 12-Luca Morisi 11-Montanna Ioane 10-Paolo Garbisi 9-Stephen Varney 8-Lorenzo Cannone 7-Michele Lamaro (captain) 6-Sebastian Negri 5-Federico Ruzza 4-Niccolo Cannone 3-Simone Ferrari 2-Giacomo Nicotera 1-Ivan Nemer
Replacements: 16-Luca Bigi 17-Danilo Fischetti 18-Pietro Ceccarelli 19-Dino Lamb 20-Giovanni Pettinelli 21-Manuel Zuliani 22-Martin Page-Relo 23-Paolo Odogwu