New Zealand are 142 for three in their second innings, chasing an improbable target of 504 to win the match, with captain Brendon McCullum (four) and Ross Taylor (20) at the crease when play resumes at the Gabba at 0930 (2330 GMT).
Neesham is scheduled to bat at number six in the lineup but New Zealand Cricket did not say whether the injury would preclude him from taking the field on Monday.
"Jimmy has worked hard to get back to fitness following his injury earlier this year, but at this stage still experiences discomfort when bowling extended loads," coach Mike Hesson said in a statement.
"Jimmy will return to New Zealand for further medical assessment and well continue to monitor his situation.
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"At this stage our number one priority is getting Jimmy fully healthy and ready for the home summer."
Left arm pace bowler Mitchell McClenaghan will join the squad in place of Neesham, Hesson added.
"Mitch has the ability to run in all day, bowl quick spells and has experience on the international stage," said Hesson.
"He'll bring a lot to the group and is obviously very excited to come and join the squad."
Neesham is the second player to suffer a back injury during the match, with opening bowler Tim Southee struggling with an "irritated disc" and looking in discomfort while batting in New Zealand's first innings.
He did not bowl in Australia's second innings and seamer Neil Wagner has been brought into the squad as cover.
(Reporting by Greg Stutchbury in Wellington; Editing by Nick Mulvenney)
