Stokes is still waiting to hear if he will be charged by police after being arrested over a late-night fracas in Bristol in September - an incident which saw him suspended by the England and Wales Cricket Board.
The Crown Prosecution Service have been handed Stokes's case by Somerset and Avon Police.
It had been 69 days since Stokes last played and he had only one practice with Canterbury after arriving in New Zealand four days ago.
On the field, the all-rounder was dismissed for two and then failed to take a wicket in his nine overs as Otago claimed a three-wicket win.
GETTY IMAGES Ben Stokes managed just two runs with the bat
Although Otago collapsed from 175-0 to 198-7, they won with 15 balls to spare. Canterbury coach Gary Stead said: "It's just general stiffness".
Anderson spoke earlier this week about the possibility of becoming vice-captain, confirming he would not rule himself out if asked but adding too that he does not see the role as a critical one - with so many experienced players on hand to help Root. It was expected he was going to be a little bit rusty.
Durham's Stokes was arrested on suspicion of causing actual bodily harm after an incident on 25 September in which a man suffered a fractured eye socket.
With a decision not to be made for several weeks, Stokes seems unlikely to play in England's current Ashes series in Australia.
United Kingdom police have finalised their investigation into the fight with prosecutors now deciding whether to charge England's vice-captain.