Whitelock played only the first half of the Crusaders' 26-27 loss to the Hurricanes in Wellington last week.
Coach Scott Robertson said it was with the longer view in mind that they decided to replace him for the second half. The injury had not recovered enough for him to play the Fijians.
Robertson believes that once over the Fijian hurdle, Whitelock can play.
"He'd love to play a little bit more. He's a little bit frustrated, but we've still got hope he's got another game or two in him."
Robertson said Whitelock set out on his final season with the side wanting to be fully involved throughout the season, but a broken hand and a concussion had restricted him to only seven games so far.
Flanker Ethan Blackadder and halfback Willi Heinz will return to the side from the bench.
Their return had been delayed a week, allowing them extra recovery time from their injuries.
Blackadder's return was especially welcomed.
"The energy he brings us at training, and when he comes on to the field, we've missed him…just his professionalism and impact he has on the game."
The Crusaders have motivation for the game, playoffs or not. The Drua scored the most famous victory in the competition when beating the Crusaders 25-24 earlier in the campaign.
But, as Robertson pointed out, the conditions won't be so tropical in a chilly Christchurch.
They had reflected on their loss earlier, but he said they had also applied some context to the situation.
The Crusaders had a stronger team, it was two months since they played in different conditions, and a quarterfinal was a different scenario.
"We're really clear on what we've got to do, we know what they will bring."
Fijian Drua coach Mick Byrne is confident his side can cause an upset if able to start well.
"We are just looking to bring a real physicality to our game because that's how our boys play well, to get on the front foot early and win the collisions.
"When we were there [Christchurch] last year, that was a large bit of Fijian community who came out in our support. We are planning to engage in more of those sorts of events this year, and plus it's the finals, so, we expect a bigger crowd supporting the Drua in Christchurch this year."
QUARTERFINAL: Crusaders v Fijian Drua, Saturday 10 June, 7.05pm, Orangetheory Stadium, Christchurch. TICKETS.
Crusaders: Will Jordan, Dallas McLeod, Braydon Ennor, Jack Goodhue, Leicester Fainga'anuku, Richie Mo'unga, Mitch Drummond, Christian Lio-Willie, Tom Christie, Sione Havili-Talitui, Quinten Strange, Scott Barrett (capt), Oli Jager, Codie Taylor, Tamaiti Williams. Reserves: Brodie McAlister, Kershawl Sykes-Martin, Reuben O'Neill, Zach Gallagher, Ethan Blackadder, Willi Heinz, Fergus Burke, Chay Fihaki