Woakes, who left the field towards the end of Pakistan's second innings at Headingley, will be assessed during the week to judge whether he will be fit for the start of the series against Australia on the June 13.
Woakes was recalled to the Test side in Leeds having been left out of the opening Test at Lord's when England preferred Mark Wood. He claimed 3 for 55 in the first innings and then removed Sarfraz Ahmed in the second before reporting discomfort.
Tom Curran, whose brother Sam made his Test debut at Headingley, was already part of the squad for the Australia series. Woakes is the second player to be withdrawn from the Scotland match after Ben Stokes picked up a hamstring strain. Stokes will also be reassessed later in the week in order to ascertain when he may be fit to return. The England management have already confirmed he will miss the first part of the Australia series.
Meanwhile, Joe Root will be among the England players returning to county action later this week as attention turns to the shorter formats of the game. Root, England's Test captain, is available for Yorkshire's home game against Northamptonshire on Thursday; a match that could yet decide which teams qualify for the knock-out stages.
Other players from England's Test squad available for Royal London Cup fixtures this week are Dom Bess (Somerset), Mark Wood (Durham), Keaton Jennings (Lancashire), Dawid Malan (Middlesex) and Sam Curran (Surrey). Malan has also been made available to play for Middlesex in their County Championship match against Leicestershire starting on June 20.
Jonny Bairstow and Jos Buttler have been rested ahead of the ODIs, while England are yet to make a decision on the county availability of James Anderson and Stuart Broad ahead of the start of the Test series against India in August. They have, however, confirmed that neither will be available for the next round of County Championship matches which starts on Saturday.
But Alastair Cook is available for Essex's Championship game against Lancashire and Moeen Ali will play for Worcestershire's final Royal London game before joining up with England's limited-overs squad.