The seamer will join up with the national side, who are preparing for the third match against India in Mohali tomorrow.
The England and Wales Cricket Board released a statement saying: "England bowler Chris Woakes has today been ruled out of the remainder of England's one-day international tour of India due to a left quadriceps strain.
"Woakes suffered the injury on Sunday during England practice in Delhi and will now undertake a rehabilitation period that rules him out of the remaining three ODIs against India.
"Durham's Graham Onions has been called into the squad as a replacement and will join the England squad in Mumbai ahead of the fourth ODI."
England have lost the first two contests against India in the five-match series.