It is a huge blow for Australia, who are already 0-2 down in the five-Test rubber. The third Test starts on August 1.
CA's Team Doctor Peter Brukner said: "James Pattinson reported some hip and back soreness on the final day of the second Ashes Test."
"We had some scans done today in London that have identified an early stage low back stress fracture. Unfortunately he will not take any further part in this Test series and will commence a rehabilitation programme with the aim to have him back for the Australian summer," Dr Brukner added.
CA's Team Performance General Manager Pat Howard said: "While we are obviously disappointed for James, the selectors have five bowlers fit and ready perform in England, providing them with many options."
"It is also important to note that several players have been performing for Australia A and are available to be called up at any stage if the NSP required them. We've been well planned to have as many bowlers fit and available in the lead-up to this important series and while this set-back for James is disappointing, we are confident we have good fast bowling depth," Howard added.
Pattinson will stay on with the squad, travelling to Sussex and then on to Manchester before returning to Australia.