Emma Kete's 61st minute strike was the difference as the Sky Blues had the better of much of the game.
England's FA Women's Super League club Chelsea now stand between Alen Stajcic's team and a place in next Sunday's final.
After a quiet opening Sydney FC were the first to make a meaningful contribution on 15 minutes.
Matilda Sam Kerr made a 30 metre run to the edge of the box where she unleashed a drive that just cleared the bar.
Then the visitors had some defensive work to do.
Sky Blues goalkeeper Casey Dumont needed to react quickly to keep the scores level just after the half hour, the former Brisbane stopper diving full length to her left to deny NTV Beleza after some inventive play inside the box.
The second half began well for Sydney FC with Ellyse Perry delivering a pinpoint cross to the head of Jodie Taylor but the effort was well saved by the NTV Beleza keeper.
Sydney's goal came just after the hour mark. A long kick from keeper Dumont bounced and fell to Kete in the final third of the field and the striker picked up the ball and chipped over the Japanese goalkeeper.
Sydney coach Alen Stajcic was well-pleased with the performance.
"To overcome the travel, playing away from home and playing a powerhouse club from a country which holds the World Cup, speaks volumes for the performance," he said.
"I'm delighted for the team. The effort and discipline they put in to today's game was outstanding.
Sydney FC will take on Chelsea Ladies FC in the semi-final at Kanko Stadium in Okayama on Wednesday night (2030 AEDT).
The winner will meet either South America's 2012 Copa Libertadores Champions Colo Colo from Chile or the Champions of the Japanese Nadeshiko league INAC Kobe Leonessa in Sunday's decider.