The South African-born batsman is to return home after scans revealed a break to a rib on his right side after he received an agonising blow from the Australian paceman at the Melbourne Cricket Ground.
The injury will take between three and five weeks to heal and the England management have opted to ensure he recovers in time for the World Cup campaign in the West Indies.
Charging down the wicket to McGrath, a tactic he used to good effect in the recent Ashes series, Pietersen was on 73 when he collapsed to the floor in agony after the blow to his right side and needed several minutes to compose himself.
He received treatment from the England physio, but he was in clear pain for the remainder of his innings before finally holing out to long-on for a defiant 82 in England's total of 242 for eight.
England said a replacement would be considered within the next 24 hours.