Watling hurt his knee during the Black Caps' defeat at Lord's and is not fit enough to line-up in Leeds on Friday.
Captain Brendon McCullum will take the gloves, having briefly deputised at HQ, while Martin Guptill will replace Watling in the side and bat at six.
With spinner Bruce Martin already ruled out of the match, former skipper Daniel Vettori is expected to play despite only joining the side on Wednesday morning.
He will face a fitness test of his own in the morning, with seamer Doug Bracewell the other option for New Zealand.
- Sports & Recreation
- Martin Guptill
- Daniel Vettori