The 26-year-old had scans on his back after the opening day of the match at the Gabba and pulled up twice on his run-in on Friday before being helped from the pitch midway through the morning session.
New Zealand Cricket later tweeted that Southee had an aggravated disc in his back and was undergoing further assessment. He failed to take the field after the lunch break, which Australia reached at 482 for three.
Hopes of a series triumph, which already looked optimistic after Australia scored a record 389-2 on Thursday, had been based in part on the potency of strike attack of Southee and left-arm quick Trent Boult.
Southee took one of the two wickets to fall on the opening day and had figures of 1-70.

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