The Serbian world number one ousted fourth seed Andy Murray in five grueling sets to set up a title match against Rafael Nadal on Sunday.
The defending champion looked to be struggling midway through the match on Rod Laver Arena as the British fourth seed battled back from a set down to take a 2-1 lead.
"I've seen a doctor and I've talked with some people," Djokovic said. I've talked with a couple of players that have a little allergy problems this year in Australia...ones they didn't have in the last couple of years but they had reactions this year.
"That's my problem. I've been trying to do everything possible to clear that out. But we are all surrounded with the flowers. It's really difficult to take that away."