Pathan, who was recovering from a side strain and skipped the Deodhar Trophy zonal one-day league competition, suffered the injury during practice last evening, a selection committee source said.
Bengal seamer Ranadeb Bose was named as Pathan's replacement in the India Seniors side.
Pathan's injury, however, was not serious and the 20-year old Baroda bowler came on as substitute for Yuvraj Singh for a brief period during India 'A' innings today.
Pathan would go through the rehabilitation work with John Gloster, the new Indian team physiotherapist.
An exact date for the bowler's return to action was not known though.