The fast bowler, 28, has suffered a recurrence of the side strain which interrupted his summer last year, ruling him out of most of the Champions Trophy and the Test series against South Africa.
But scans have shown that the injury is a “very minor” left side strain which should not keep him out for long.
Leg spinner Mason Crane, 20, will take Woakes’s place as England look to land a late blow on Australian flanks here at the Sydney Cricket Ground starting Wednesday night UK time.
And while captain Joe Root is looking forward to seeing how the Test debutant goes, he acknowledged that the injury was a blow.
“He pulled up a bit sore form the last game and it is obviously quite an important area for any fast bowler so it is important we look after that and make sure he is 100 per cent,” he said.
“He is obviously an integral part of both white ball and the Test team and it is important he doesn’t have another setback like he did in the summer.
“It is the same one so more than anything it is about making sure he is not out for a significant period of time like he was throughout the summer,” he said.
Woakes sustained the original injury in June during the opening match of the Champions Trophy and made his return in August for one Test before being benched again for the final match of that series.
As a result of Woakes’s injury Tom Curran retains his place in the side as does the out of form Moeen Ali, who will adds muscle to a batting line up weakened by the loss of the all-rounder.
But it is Crane who will create the most excitement.
“Mason has bowled well when he has had the opportunities on this trip and it is a really good chance for him to show what he is capable of and on this surface he is going to be a really good option,” said Root.
“It looks like it should give a big of turn throughout. Generally does here anyway but it looks like it has definitely dried out in the last 24 hours. It should spin anyway.”