England lead the five-match series 2-1, with hosts India at 204-6 at the end of day one of the final test at The Oval on Thursday.
Woakes picked up the injury after falling heavily as he dived to try to prevent a boundary by Karun Nair at long-off.
"England seamer Chris Woakes will continue to be monitored throughout the remainder of the Rothesay Fifth Test at The Kia Oval, following a left shoulder injury sustained on day one of the match against India," ECB said in a statement.
"At this stage, the injury has ruled him out of any further participation in the Test.
"A further assessment will be conducted at the conclusion of the series."
Woakes had bowled 14 overs while conceding 46 runs on Thursday and took out India opener KL Rahul for his only wicket of the day.
England are already without captain and all-rounder Ben Stokes, also due to a shoulder injury.