Jan Vennegoor of Hesselink had seemed to send the champions on their way in the 24th minute when he rose above a crowd of players at the near post to glance Nakamura's delicately flighted corner home at the far post.
The noise that greeted the goal almost took the roof off the stand, but Killie refused to buckle and created the better chances in the remainder of the half.
They almost made an instant response when Peter Leven got goal-side of Nakamura, but headed over the bar from a great position.
Steven Naismith had an even clearer chance in first-half stoppage time when Grant Murray intelligently nodded the ball into his path, but the striker scuffed his effort tamely into Artur Boruc's hands.
Celtic were screaming for a penalty three minutes after the interval when Thomas Gravesen's shot seemed to be blocked by the arm of Momo Sylla, and they were stunned two minutes later when Killie equalised with a lovely goal.
Gary Locke's pass sent Gary Wales past Daren O'Dea and into the box where he picked out Colin Nish, who made no mistake.
Both sides were looking for a winner in an engrossing second half, and it looked like the Hoops would have to wait another week for their party until Nakamura was fouled on the right side of the box in injury time.
The Japanese midfielder then coolly floated the ball past Alan Combe into the far corner for a spectacular title clincher.