Williamson faced Australia in a warm-up match prior to the ICC Men's T20 World Cup Super-12s. He led New Zealand in scoring with 37 off 30 balls while also aggravating his elbow.
The coach hinted that left-arm spinner Ajaz Patel is likely to be dropped from the final XI to make way for Wagner.
Coach Gary Stead confirmed Ferguson would return home to New Zealand in the coming days.
New Zealand coach Gary Stead said the composition of the squad followed a "horses-for courses" type strategy and took into account the recent history of touring teams visiting Sri Lanka -- particularly England and South Africa.
England amassed 26 boundaries in total in the entire duration of the match as compared to 17 by the Black Caps and were thus crowned as champions as per the rules of a Super Over tie.
Ferguson has been a standout performer for New Zealand in the tournament as they finished fourth in the standings, taking 17 wickets to sit joint-third in the table for the most wickets taken.
In the 2nd ODI, Kiwi batsmen failed to build a partnership at the top.
