Pattinson, 20, was called into the squad after Josh Hazlewood was ruled out and will be now replaced by John Hastings.
"During the past week, James has complained of some back stifness during preparation for the second Test," tour physio Kevin Sims was quoted as saying by the 'Herald Sun' today.
"James' symptoms were consistent with a low back bone stress injury and scans have confirmed the early stages of a low back stress fracture.
"He has therefore been withdrawn from the one-day squad as he will require a period of rest from bowling.
"He will be closely monitored by Victorian and Cricket Australia medical staff to determine his return to cricket."
The pacer, with only four first-class matches for Victoria under his belt, has impressed many with his pace and ability to swing the ball. "It is disappointing for James Pattinson to suffer an injury at this stage, however it does present a great opportunity for John (Hastings) to show his potential at international level prior to selection for the 2011 ICC Cricket World Cup on the subcontinent," Chairman of selectors Andrew Hilditch said. Australia will play three ODIs against India starting October 17.