Once again, the Phoenix will rue what might have been.
Although Sydney were the better side across the contest, the Phoenix conceded two sloppy goals, which eased the pressure on the home side.
They also found their cutting edge too late, only getting going offensively after falling two goals behind.
For most of the match Phoenix struggled to find any rhythm with the ball, too often forced to play square or backwards under Sydney pressure.
They also lost goalkeeper Oli Sail to a hip flexor injury midway through the first half, though Alex Paulsen looked competent on debut.
It was another harsh lesson for this young Phoenix group, who continue to show glimpses of their potential but lack creativity on attack, along with the required defensive resilience.
Fullback James McGarry wasn't considered due to a knee injury, while Gary Hooper was unavailable for personal reasons.
After his two goals midweek in the FFA Cup, Jaushua Sotirio was rewarded with a start while Ben Waine and Louis Fenton were also retained from that victory.
Sydney winger Elvis Kamsoba should have opened the scoring in the 15th minute, blazing over from 12 yards, though Fenton did well to put the Sydney FC player off.
The Burundi-born Kamsoba made up for his miss five minutes later, slamming home from close range, after he was left free at the near post. It was a soft goal to concede, with the Phoenix caught ball watching after Sydney kept the ball alive in the penalty area.
In the 27th minute Sail limped off with a hip flexor problem, with 19-year-old Paulsen introduced for his A-League debut.
The rookie was forced into a strong near-post save from Kamsoba, before Patrick Yazbek tested him from distance from the resultant corner.
The Phoenix created precious little in the first 45 minutes. They looked out of sync in the final third, struggling to find any space or time, while Reno Piscopo was shut down effectively.
They were sharper after the break, pressing higher, winning possession and looking more constructive, as the fullbacks began to get forward and Piscopo and Sotirio started to link.
But they paid a heavy price for being over-enthusiastic with their press, losing their shape, which led to Adam Le Fondre extending Sydney's lead in the 60th minute.
It was cruel, virtually Sydney's first chance of the second spell, as they counterattacked quickly, though Le Fondre did well to elude Sam Sutton, who had a chance to clear.
Sydney had further opportunities, before the Phoenix clicked in the final 20 minutes.
Nicholas Pennington, Ben Old and Oskar van Hattum all made an impact from the bench, while Waine had a couple of half chances before his 83rd-minute goal.
The 20-year-old was quickest to react in the area, turning nicely and slotting past Andrew Redmayne.
But that was as good as it got, despite some promising forays, as Sydney FC hung on.
Sydney FC 2 (Elvis Kamsoba 20', Adam Le Fondre 58')
Wellington Phoenix 1 (Ben Waine 83')
Halftime 1-0
