Batsman Michael Clarke, who deputised for Ponting in a Twenty20 match against New Zealand last year, will lead the side at the MCG.
Ponting was troubled by pain and stiffness in the lower back during the fourth Test against India in Adelaide this week.
"He pulled up pretty sore this morning," Nielsen told reporters on Friday. "His back is just not 100 per cent.
"With the uncertain nature of Twenty20 cricket and the frantic nature of it we're just a bit concerned that if he has to dive in the first over if we're fielding and pulls up very sore it could leave us one short."
Brad Hodge will bat at number three for Australia with batsman David Hussey set to make his debut.