Kaino received a blow to his shoulder during the game but continued to play thinking it would settle. Investigations later revealed a piece of bone had been knocked off the joint.
A shoulder specialist has advised surgery, which Kaino will have on Wednesday, keeping him out of rugby for about six months.
"I'm gutted. I really didn't think this was going to take me out of the whole Blues season. It certainly helped seeing the guys have a good win at Loftus in the weekend,'' said Kaino, who was judged the All Blacks' best player last year.
From South Africa, Blues coach Pat Lam said Kaino's season-ending injury was quite a shock.
"Jerome is a great player and brings a lot to the Blues on and off the field. This is a real blow for him and I know, like us, he is really disappointed that he won't be playing this season with the team. All of us wish him well for the surgery on Wednesday.''
The Blues beat the Bulls 29-23 at Loftus Versfeld, 20-year-old first-five Gareth Anscombe scoring all of his side's points in his first start.
Lam is waiting to hear of the sanction for wing Rene Ranger, who was cited for a dangerous tackle late in the match and could face a suspension.
