The 31-year-old left-hander has been in electric form at the top of the innings but took a knock during training before the back-to-back games against Central Districts in New Plymouth earlier this week.
He felt fine at the time but woke up feeling ill the morning after the second fixture and would take a week off, Otago coach Rob Walter said.
"He took a blow during training but it didn’t seem too significant at all, really," Walter said.
"But he has had a few knocks before, so this is really about being cautious and making the right decision.
"He went to see the doctor and he said it was best to take a week off from a precaution point of view."
Rutherford had headaches and was feeling fatigued.
He has a history with concussion.
Five years ago, he had three months off after he was hit by Scott Kuggeleijn.
This is Rutherford’s fifth lay-off for concussion during his career.
But earlier this year he told the Otago Daily Times he was "at ease" with his decision to continue playing and that there were "some really good guidelines in place".
In Rutherford’s absence Nick Kelly will open the batting and assume the captaincy, while form Otago A batsman Llew Johnson has been called into the side.
Pace bowler Michael Rae returns from New Zealand A duty to bolster the bowling line-up in the only other change from the side which beat Central Districts by 10 runs at Pukekura Park on Tuesday evening.
"It is safe to say Rutherford was the difference in both games for us, particularly in the first one [when he scored 97].
"You can’t just replace someone like that but, as is always the case, it presents another opportunity."
Johnson may get that opportunity.
He is likely to be battling for a start alongside all-rounder Angus McKenzie.
If Johnson does get the nod, he will take some good form into the game.
The 20-year-old has scored a century for Otago A this season and smashed a double hundred in club cricket.
He made his debut for the province as a 17-year-old during the T20 in Alexandra and played three games with little success.
"He has been knocking really hard on the door and it is great to pick guys who are in form.
"One thing that stands out is his game has actually grown fairly significantly in terms of his understanding and the shot options that he has.
"He has really started to develop the art of batting and understanding how he needs to bat in different game scenarios."
