The Matildas star limped out of the derby tie within just the first 20 minutes of City's 2-0 home defeat after requiring several minutes of treatment on the Joie Stadium pitch after she appeared to wrench her right knee while overstretching for the ball.
There was much concern from the City medics before the 22-year-old was able to get back to her feet and, briefly, it appeared as if she felt she might be able to get back into the action.
But she was substituted in the 24th minute by Naomi Layzell, and could only watch on the bench as her dream of any English silverware this season died.
Fowler was still being treated when the already injury-depleted City went 2-0 down to United, with Grace Clinton adding the second in the 22nd minute after Celin Bizet had netted brilliantly after six minutes.
It was a dispiriting end to what had been an another impressive week for Fowler when she netted for the Matildas in their win over South Korea.
It ended any prospect of Australia's two premier women's players going head-to-head in the Cup final in May, with Sam Kerr's Chelsea having reached the final with a 2-1 win over Liverpool on Saturday.
Kerr herself faces a race against time to be fit for the final as Chelsea have reported she's still "a few weeks away" from getting back into action after her own long-standing ACL injury.
Holders United looks set to offer a big challenge to the English champions Chelsea after reaching their third final in a row.
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