The final major of the year gets under way next Thursday at the Valhalla Golf Club in Louisville, Kentucky.
But McGinley, whose best major performance came at the 2004 event when he tied sixth, will not be able to play alongside any potential Ryder Cup colleagues as the fight for places at Gleneagles intensifies.
"The scan showed that I really needed to rest my shoulder for a couple of months," McGinley said.
"It's a pity because I would have loved to have teed up at Valhalla.
"But I assessed the situation over the past couple of weeks during my family holiday and I think this is the sensible decision.
"It's not just during the week of the tournament itself that is the problem, it is the fact that the injury also hampers my normal preparation for events.
"And you do not want to be going into any tournament - far less a major championship - not properly prepared."