The same injury had kept the batsman out of the last two ODIs against the Kiwis also.
Dilshan's unbeaten century in the third One-dayer helped Sri Lanka take a winning lead in the five-match and rain affected series.
Sri Lankan team manager Charith Senanayake said Dimuth Karunaratne would replace Dilshan in the squad and would open the innings with Taranga Paranavithana.
The 24-year-old left handed batsman Karunaratne has earlier represented Sri Lanka in two ODIs, both during Sri Lanka's tour of England in 2011.