The pair, who won the calendar year Grand Slam in 2014, were beaten 6-4 1-6 6-4 by Dutch second seeds Jiske Griffioen and Aniek van Koot.
Scotland’s Gordon Reid saw the defence of his men’s singles title ended in the last four.
Reid found world number one Shingo Kunieda too strong, losing 6-2 6-1.
Whiley and Kamiji, who were also beaten in last year’s final, had defeated the Dutch pair at the French Open, Wimbledon and US Open finals last year.
“Obviously I am disappointed that we lost the final today. Neither Yui nor I played like we can,” admitted Whiley, who had lost to Kamiji in the singles semi-finals on Thursday.
“But now we know what we need to do to win the Australian Open.”