His exclusion was the main talking point before play in the first test between New Zealand and South Africa at the University Oval yesterday.
The Black Caps opted to play their two specialist spinners, Mitchell Santner and Jeetan Patel, instead.
It is the first time New Zealand has tried that tactic on home soil since 2010, when Patel combined with Daniel Vettori. Coincidentally, it was also the last time Patel played a home test.
It was a bold tactic but it appears to be the right move.
The pitch is slow and the bounce was inconsistent, particularly early on. Patel and Santner bowler well, albeit without success, and helped restrict South Africa to 229 for four from 90 overs.
Once the decision was made to play both spinners, it was either Southee or Neil Wagner who would have to sit out the test.
''It was certainly something that Kane [Williamson], myself and the senior players spent a bit of time tossing over,'' Black Caps coach Mike Hesson said.
''No matter which way we went it would have been a difficult decision.
''We needed one of the two seamers to be able to try and create things when there is not a lot on offer, and Neil has certainly done that consistently over the last few years.''
South Africa opener Dean Elgar moved the focus off Southee's omission with a tenacious and undefeated 128.
But he was also caught by surprise when Southee's name was missing from the playing XI.
''I was actually, because he is your trump card. Him and [Trent] Boult have been phenomenal for New Zealand in test cricket and one-day cricket. So I was a little surprised to see him not playing.''
While South Africa had the better of the day, it has not taken the game away from the Black Caps.
''They certainly haven't got away from us,'' Hesson said.
''I think the first hour tomorrow will be critical. Hopefully we'll make use of that new ball.''
