Fowler and Aivi Luik were both ruled out of Thursday night's game at Suncorp Stadium after suffering concussions in separate incidents in Tuesday's closed training.
The pair join superstar captain Sam Kerr (calf) and veteran striker Kyah Simon (knee) on the sidelines.
Van Egmond's inclusion, likely as the No.10 attacking midfielder, pushes Caitlin Foord into the main striker role.
Alanna Kennedy and Clare Hunt remain as the starting central defenders despite the former having a limited training week.
Kerr and Simon are both named on Australia's bench but clearly won't feature.
Nigeria and Barcelona star Asisat Oshoala isn't starting but has been named on the bench.
Australia (three points) can seal progression to the knockout stages with victory over Nigeria (one).
A draw or defeat would mean their fate comes down to Monday's final group match against Canada at AAMI Park, when Fowler and Luik should both be available but Kerr appears less likely to feature.
MATILDAS STARTING XI
Mackenzie Arnold (GK), Steph Catley, Alanna Kennedy, Clare Hunt, Ellie Carpenter, Katrina Gorry, Kyra Cooney Cross, Hayley Raso, Cortnee Vine, Emily van Egmond, Caitlin Foord.
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