He had been comfortably the pick of the New Zealand bowlers on a dismal opening day when Australia rattled up a Gabba first day record 389 runs.
By the time they settle into Perth on Tuesday night for the second test starting on Friday, New Zealand's squad will include Trent Boult, Matt Henry, Doug Bracewell, Neil Wagner and now Mitch McClenaghan, plus the problematic Southee.
Neesham joins fellow allrounder Corey Anderson (back), ODI international Ben Wheeler (back) and Adam Milne (shins) on the injured list, although Milne is due to play a T20 match for Central Districts against Auckland in New Plymouth on Wednesday.
Left armer Wheeler and the slippery Milne are yet to play a test, as is the big, bustling McClenaghan, whose credentials are based around his tidy ODI record of 76 wickets in 43 games.
New Zealand have some hard thinking to do ahead of Perth, a notoriously bouncy, fast pitch.
After their bowlers were flayed for 820 for eight at the Gabba, coach Mike Hesson and captain Brendon McCullum need to ponder whether they need extra pace support for Boult, who was below his best in this test, and/or as cover in case Southee, should they take a punt and pick him, breaks down again.
A Neesham or Anderson would give that backup with the ball, although the issue of loading limits their usefulness.
With fitness a priority, some bowlers are restricted in their output during a day in the field.
New Zealand's numbers are still good, but they certainly don't need another one or two falling over at this early stage of a season which will extend into the world T20 tournament in India in March.
How New Zealand's seam bowling stocks sit
Tim Southee: Irritated disc in his back, suffered on the first day at the Gabba. A wait and see situation with the second test starting in Perth on Friday.
Trent Boult: Fit but bowled below his best at the Gabba.
Doug Bracewell: Fit, but largely ineffective in the first test.
Matt Henry: Fit, but not selected for the Gabba.
Neil Wagner: Coming across to Perth as cover for Southee. A fit and irrepressibly enthusiastic left armer.
Mitch McClenaghan: Uncapped in tests, bustling left armer with decent ODI record. Replacement for Jimmy Neesham.
Corey Anderson: Back problems. Unfit.
Jimmy Neesham: Back problem flared up in this test. Flying home.
Ben Wheeler: Back problems. Sidelined. Promising left armer, has played limited overs internationals.
Adam Milne: The quickest of the lot. Due to return from more shin problems and play for Central Districts against Auckland in a T20 tomorrow. Uncapped in tests.