Adelaide produced an upset by beating Brisbane Roar in the Elimination Finals but could not replicate that performance in its semi-final against the Sky Blues.
Adam Le Fondre was on target when the sides met in the regular season last month and converted from the penalty spot to put the hosts ahead in Saturday's clash.
Brazilian striker Bobo added a second before half-time and Sydney FC held on, despite Le Fondre's penalty miss and Juande's stunning strike to set up a nervy finish.
The home team was awarded a 24th-minute penalty for James Delianov's challenge on Kosta Barbarouses, with Le Fondre sending the goalkeeper the wrong way from 12 yards.
Bobo doubled his side's advantage with a sliding first-time shot to round off a well-crafted move just before the break.
It looked like being plain sailing for Sydney when Javi Lopez took out Barbarouses in the box, but Le Fondre's penalty was saved by Delianov and that sparked an Adelaide revival.
Tomi Juric's free-kick hit the Sydney wall but Juande thumped in the loose ball from 20 yards with a little over 25 minutes still to play.
Thomas Heward-Belle was required to keep out efforts from Juric and Jordan Elsey, but Sydney held on to reach its third final in a row and a fifth in seven years.
Melbourne City and Macarthur FC meet in the other semi-final on Sunday.