Fernando was warned twice for running on the pitch during the 81-run win over the Black Caps at Sabina Park on Tuesday while his five overs cost 45 runs.
Sri Lanka's chief selector Asantha de Mel told the BBC they were not happy with Fernando's form and that fellow seamer Farveez Maharoof is likely to get the nod.
"Most probably it will be Maharoof," said De Mel from the Caribbean. "We were not satisfied with Dilhara's performance."
Maharoof was considered unlucky not to make the semi-final after he had taken 4-25 in Sri Lanka's last Super Eights game against Ireland.
De Mel also confirmed that Upul Tharanga would continue to open ahead of former skipper Marvan Atapattu.
If Atapattu doesn't play it will be the second time he has sat out an entire World Cup tournament.
The same fate befell him when Sri Lanka won the title in 1996.