Captain Brendon McCullum will take the gloves, and Martin Guptill returns to bat at six. McCullum moves down to seven.
Watling appeared to move freely in training at Headingley but a call on his availability was made immediately afterwards.
Vice-captain Kane Williamson said Watling made the decision himself.
"He's still not 100 per cent. It's a shame because he's been keeping outstandingly in some of cricket's toughest conditions with the ball moving around. His runs will be missed."
In the seven of his 14 tests he has played as wicketkeeper Watling has 22 dismissals, all catches. That's two dismissals per innings. The next best, of the 28 players to have kept for New Zealand, is Brendon McCullum on 1.849.
The dismissals-per-innings figure is not the definitive wicketkeeping quality but it indicates Watling rarely fluffs his lines. Byes are also uncommon too. Before the second innings when he got injured, Watling had given away one bye every 221 balls or 36.5 overs. It suggests a level of concentration seldom thwarted.
Before Watling's demise most observers had focused their field glasses on Daniel Vettori. All signs indicate he will replace Bruce Martin.
Physiotherapist Paul Close, strength and conditioning coach Chris Donaldson and ultimately coach Mike Hesson will assess his performance in further detail after the final training.
Hesson decided against Vettori speaking to media because he is still not officially part of the test squad, but that seems a technicality. Sporting a beard that could have seen him audition for Castaway, he threw, caught, bowled and batted for more than two hours.
Bowling was the focal point. Vettori spent just over half an hour striding in. He landed the ball on a good length the majority of the spell and got the odd one to purchase on the practice strips cut 50m from the match pitch.
His batting assumed its familiar shape with a full range of on drive slaps, front of square swats and paddles behind square.
Williamson said Vettori's 16 years of experience was welcomed back.
"He looked great, he's done it for so long, we'll see how his body shapes up tomorrow and whether he's ready."
The news also brightened Neil Wagner's day.
"Walking in the changing room and seeing him there was massive. It will be good to see him back in action.
"He's been getting himself ready for the [Champions Trophy] one-dayers so I don't think he'll be too short on bowling. He looked fine in the nets, like the normal Dan Vettori. I won't be surprised if he rocks up and takes a five-for.
"Knowing that he's hopefully going to be standing next to you at mid-off where you can have a chat and pick his brains is nice."
- Andrew Alderson in Leeds
