The seeding heat was won by Filepe Toledo with a score of 11.93 (5.83, 6.10) from fellow Brazilian Deivid Silva on 6.07 (3.30, 2.77) and Christie on 4.10 (1.57, 2.53).
Christie's injury was made all the more frustrating in that he would have only needed a 3.55 wave to advance.
Christie, if able to continue, faces a two-man elimination heat — a must-win or his season is over.
He went into Pipeline ranked 33rd. The top 22 after this contest retain their places for the 2020 CT.
Several surfers, including fourth-ranked Toledo, are in the hunt to win the world title.
Brazil's Italo Ferreira leads the standings from fellow countryman Gabriel Medina and South African Jordy Smith.
The Pipeline is also the final contest of surfing's Triple Crown led by Australian Ethan Ewing.