Cilic, who took his best game to Nadal before the injury, will face British up-and-comer Kyle Edmund in the semi-final.
The incident appeared to fire Edmund up but it was not enough for him to overcome his rival's deadly serve, as the Croatian prevailed in straight sets.
Wozniacki had an early break in the deciding set to take a 4-2 lead, then broke again in the seventh game before serving out the match in 2 hours, 11 minutes.
With both players holding serve throughout, the set would be decided in a tie-breaker with Cilic taking it 7-4.
However, though Cilic has had some lengthy battles in Melbourne - including a five-set thriller with Rafael Nadal - he's feeling physically good and with a two-day rest period, he's confident of being 100%.
It'll be a third major final for Cilic, who beat Federer in the semifinals at the 2014 U.S. Open before going on to win his breakthrough Grand Slam title. She won a 27-point rally while holding serve in the fourth game of the second set, then hit a backhand victor into the open corner to break Svitolina in the next game for a 5-0 lead.
In another shock result, Kyle Edmund from Britain overcame world number three Grigor Dimitrov in four sets, booking his place in the semifinals for the first time in his career.
Edmund looked strong to start the match, coming at Cilic playing a very aggressive game. "His movement was a little bit restricted so I just tried to keep moving the ball around".
"It is not the first time an opportunity has gone for me but I am a positive person, and I can be positive, but today is an opportunity lost to be in the semifinals of a Grand Slam and fight for an important title for me".
Nadal withdrew from tournaments at the end of last season due to an ongoing knee injury that also forced him out of this year's Brisbane International.
ELISE MERTENS, world No. 37, on retired tennis star Kim Clijsters following her match in the middle of the night back home.