Mayweather won a unanimous decision in the four-belt unification bout to improve his record to 48-0.
The injury would appear to rule out any chance of a rematch after the 38-year-old Mayweather said he would have one more fight in September before retiring.
"We have an MRI scan that confirms he has a rotator cuff tear. He has a significant tear," orthopedic surgeon Neal ElAttrache told ESPN.com.
Pacquiao (57-6-2, 38 KOs), known for his aggressive and all-out attacking style, was clearly not the his typical offensive-minded self in Las Vegas.
After the fight, Top Rank promoter Bob Arum said Pacquiao suffered a shoulder injury in training camp about two-and-a-half weeks earlier and that it hampered him in the fight.
Top Rank and Pacquiao confirmed the account of the injury in a statement on Monday, saying that the 36-year-old and his doctors had concluded that with rest, treatments and monitoring, he would be ready for the fight.
However, they said the Nevada Commission stopped the treatment a few hours before the fight, telling them it was unaware of the shoulder injury.
(Reporting by Cameron French; Editing by John O'Brien)
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