"Consumer guarantee rights under the Australian Consumer Law exist independently of any manufacturer's warranty and are not extinguished simply because a consumer has goods repaired by a third party," ACCC Chairman Rod Sims said in a statement.
An Apple spokeswoman did not immediately respond to an email requesting comment.
The regulator said that between September 2014 and February 2016, Apple customers who downloaded software updates then connected their devices to their computers received a message saying the device "could not be restored and the device had stopped functioning".
Customers then asked Apple to fix their devices, only to be told by the company that "no Apple entity ... was required to, or would, provide a remedy" for free, the documents added.
Apple engaged in "misleading or deceptive conduct and made false or misleading representations to consumers" about its software updates and customers' rights to have their products repaired by the company, the commission said.
As well as fines, the ACCC said it was seeking injunctions, declarations, compliance programme orders, corrective notices, and costs.
The lawsuit was filed late on Wednesday, a week after the consumer watchdog granted Apple a win by denying Australia's banks the right to introduce a mobile payment system to rival its Apple Wallet.