The top-seeded Australian now meets qualifier Ivo Minar, who beat fellow Czech Radek Stepanek 6-1, 6-2 to reach his first ATP final.
Russian third seed Elena Dementieva pulled out of the women's semi-finals due to illness, giving unseeded Australian Samantha Stosur a free ride into the final.
World number one Lindsay Davenport also withdrew from her quarter-final against Stosur the previous day.
Stosur, runner-up at last week's Australian hardcourt championship on the Gold Coast, now faces fellow countrywoman Alicia Molik or Chinese amateur Peng Shuai.
Minar, 20, ranked 158th in the world, was planning to
"For me, it's a great experience. This is the best result of my career," Minar told a news conference.
"Now I am in the final I will play."
Mirnyi had beaten Hewitt in two of their previous three meetings, including the first round of the 2000 Sydney Olympics on the same court, and looked set for another win over the Australian when he took the opening set on a tiebreak.
But Hewitt, who has won the Sydney title three times, broke serve twice to square the match before running away with the deciding set.
Mirnyi's last two opponents had quit halfway through the first set and Hewitt's extra time on court proved decisive as he twice broke serve in the decider.
