Woakes missed a significant part of England's home season after straining his side in the opening match of last year's Champions Trophy and pulled up sore after the fourth test in Melbourne last week.
The 27-year-old's enforced absence will be the only change to Root's side for the test at the Sydney Cricket Ground (SCG), which starts on Thursday.
"He's obviously an integral significant member of both the white ball and test team and it's important he's not out for a long time like he was last summer," Root told reporters.
"He's going to miss this week and it's a great opportunity for Mason to come in and make his debut."
Woakes's injury has probably resulted in a reprieve for out-of-form all-rounder Moeen Ali, who had been expected to make way for 20-year-old Crane.
England have already handed back the Ashes after losing the first three tests of the series but Root has made it clear the tourists would not be handing out test caps in Sydney willy nilly, as they did at the end of the 2013-14 whitewash.
Crane, who played at the SCG for New South Wales last year during a highly successful stint with the Gordon club, will become the youngest England spinner to make his test debut for 90 years.
"He's been outstanding. For a young man to apply himself and absorb himself in the environment as he has, is exactly what you want," Root said.
"You can see a big progression in his game since he's been involved in this tour. He's right up for international cricket and he's not someone who's going to back down.
"On this surface, he's going to be a really good option. It looks like it's going to give a bit of turn throughout."
Team: Alastair Cook, Mark Stoneman, James Vince, Joe Root (captain), Dawid Malan, Jonny Bairstow, Moeen Ali, Tom Curran, Stuart Broad, Mason Crane, James Anderson
(Reporting by Nick Mulvenney, Editing by Greg Stutchbury)
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