The Blues released a statement saying Haddin was withdrawn from the match to balance his workload with international and domestic matches on the horizon.
"Brad has withdrawn from this match on the basis of balancing his workload returning from injury, particularly in light of the short turnaround between games," the statement said.
"Brad will re-join the squad for the next round of Sheffield Shield and Ryobi Cup matches commencing in Tasmania next week."
Haddin is in line to be included in the Australian Test squad for the upcoming tour of India.
Peter Nevill will now take over the wicketkeeping duties against WA, while Nic Maddinson comes into the side.