Jamie Cripps has replaced him in the side and will play his sixth game for the season.
Kennedy left the track early from Saturday's light training session at Wesley College in Melbourne with a suspected calf complaint.
However the Eagles denied there was a problem until team sheets were lodged.
Kennedy is a huge loss for the Eagles in a season defining game. He has kicked 34 goals and has been one of the few West Coast stars to deliver consistently this season.
The Eagles' tall forward line was expected to stretch the undersized Saints, who have made no secret of their need for tall players in the back half.
Kennedy's loss adds to the Eagles' woes on the injury front.
They are already missing skipper and champion full back Darren Glass and sharp shooting Mark Le Cras, who experienced soreness in the arm he broke in 2012.
