His victory was only the second occasion, after Steve Waugh won in 2001, when the medallist did not win either of the Test or one-day player awards.
Martyn, who scored six centuries in 2004, won the Test award, while Clarke was pipped by Andrew Symonds for the one-day award.
Clarke scored 151 on his Test debut against India in Bangalore in October and claimed 6-9 with his left-arm spinners in the same series in India. He then produced 141 in his first Test in Australia against New Zealand in Brisbane in November.