Cummins took 1 for 53 in his 10 overs in the first match, having England captain Alastair Cook caught behind, but pulled up with pain after the game and has been diagnosed with a medium-grade strain.
Australian team doctor John Orchard, said: "Pat sustained an abdominal muscle strain on his left side during the first ODI at Lord's. Whilst he was able to complete his ten overs, he was sore after the game and was scanned, the results of which have revealed a medium grade side-strain. This will keep him out of the remainder of the England tour. His return to cricket will be decided in due course, based on follow-up examinations in Australia."
Cummins will fly home to Australia on Monday and the selectors have decided against calling up a replacement player to the squad. Brett Lee and Clint McKay formed a three-man pace attack at Lord's, while Ben Hilfenhaus, Mitchell Johnson and James Pattinson are the other quicks in the squad.
This tour marked Cummins' return to the international scene following the foot injury he picked up on the tour to South Africa last November, which kept him out of action for the whole of the Australian season. The side strain will put his place on the A-tour to England, which follows the one-day series, in doubt.