Woakes is now a doubt to face Australia this summer.
Sam Curran was handed a debut in his place on Friday, the Surrey teenager named in the team at Headingley having only joined up with the squad as injury cover earlier in the week.
Stokes will miss next weekend's ODI against Scotland and will be replaced by uncapped batsman Dawid Malan.
An assessment is due this week to figure out if he can be fit in time for the upcoming five-match ODI series against Australia, starting June 13.
England seamer Chris Woakes has joined Ben Stokes on the injury list for next weekend's one-day global against Scotland. A similar injury ruled Woakes out of the final leg of the ODI series against South Africa in 2017.
The 29-year-old bagged four wickets before he was forced to leave the field with tightness in his right quad at the end of the Pakistan's second innings during the drawn second Test of the two-match series against England.
He will not be involved against Scotland this Sunday and a decision over his participation against Australia will be determined following further fitness tests this week.
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