Woakes, who took 9-36 for Warwickshire this week, has been selected ahead of uncapped pace bowler Jake Ball for Friday's match at Chester-le-Street.
Captain Alastair Cook said Woakes, 27, will bat at number eight.
"I don't think we have seen the best of him in an England shirt but he is in fine form," said Cook, who needs 20 runs to reach 10,000 in Tests.
Stokes, 24, will miss the remainder of the three-Test series after knee surgery following the innings-and-88-run victory in the first Test at Headingley.
Wicketkeeper Jonny Bairstow, who was named man of the match at Leeds for his 140 and nine catches, is set to be promoted one place in the batting order to six, with all-rounder Moeen Ali moving up to seven.
Seamer Woakes, who has taken eight wickets at 63.75 and scored 129 runs at 21.50 in six Tests, returned combined figures of 2-197 in two matches during England's 2-1 Test series win in South Africa.