Johnson has a slight Achilles injury, and head coach Clive Woodward said: "Martin will not play any part in the game against Italy.
"He has an Achilles injury, which with a brief period of rest should be fine in time for the game against Scotland.
"I'm obviously disappointed for Martin but it's essential that he is 100% fit if he is to be considered for the Scotland match."
Woodward revealed: "Jonny Wilkinson will captain England for the first time against Italy with Lawrence Dallaglio acting as vice-captain.
"This is a huge honour for Jonny. He's been vice-captain for a number of internationals, captained his club Newcastle Falcons and I know it's a challenge he will relish."