The result meant Australia finished on top of Group A with a perfect nine points from nine and a goal difference of plus 13.
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To qualify for the Olympics, Australia must now beat Uzbekistan in a two-legged play-off in February.
Uzbekistan will host the first game on Feb. 24, with Australian to host game two at a yet-to-be-decided venue on Feb. 28.
The Matildas were a dominant force during their three games in Perth, but it took them until the 62nd minute to break down Chinese Taipei's stubborn defence on Wednesday night.
It was well worth the wait for the sell-out crowd.
Fowler trapped a floated pass and took one more touch before unleashing a powerful strike from 20m to send the fans wild.
Hometown hero Kerr scored from point-blank range six minutes later to keep the ball rolling, before substitute Tameka Yallop sealed the deal in the 76th minute.
"I think in those moments, you're not really thinking too much," Fowler said of her wonder strike. "You're just doing them off instinct and trying them out.
"Sometimes they work, sometimes they don't. I had a few chances in the first half and that one in the second half went in."
But despite registering 17 shots to one in the first half and enjoying 79 percent possession, the Matildas couldn't find a way past Chinese Taipei's staunch defence.
Fowler came the closest in the 14th minute, but her powerful shot from close range rattled the woodwork and deflected away.
Chinese Taipei goalkeeper Cheng Ssu-Yu pulled off a series of strong saves to further frustrate the Matildas.
But Australia had only themselves to blame on other occasions, firing a series of shots either wide or over the target.
Kerr had a golden chance to open the scoring on the stroke of half-time, but her header at the far post flew over.
The Chelsea striker also fluffed a chance early in the second half when a poor first touch cost her what would have been a one-on-one opportunity against the goalkeeper.
But there was no stopping Fowler's thunderous strike in the 62nd minute.
And when a goalmouth scramble ensued six minutes later, Kerr was on hand to put away the easy tap-in.
It made it five goals for Kerr across the three qualifiers, and also marked the Matildas' 900th goal.
Kerr was subbed off straight after the goal, but Yallop ensured the party continued with an easy tap-in following good lead-in work from Caitlin Foord and Amy Sayer.
In the other match in Perth on Wednesday, the Philippines beat Iran 1-0 courtesy of a 19th-minute goal from Tahnai Annis.