The Wellington Phoenix will have to do it the hard way in the A-League playoffs.

After losing 2-1 to Sydney FC at Westpac Stadium tonight they were consigned to a fourth-place finish on the ladder, which means they will host Melbourne City in the opening round of the knockout stages before having to go on the road if they advance.

A win over Sydney FC would have pushed Wellington to second and given them a bye to start the playoffs before hosting a semifinal in two weeks.

Last weekend, the Phoenix came back from 2-0 down to beat the Central Coast Mariners 3-2 in thrilling fashion but there were no such heroics this time around.

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At one point this season, the Phoenix looked on track to claim a maiden Premiers Plate so they may view fourth place as a disappointment.

There were changes across the paddock today as Sydney FC were without striker Marc Janko who stayed in Australia with a minor injury. The Austrian leads the golden boot standings with 16 goals.

Phoenix coach Ernie Merrick took the chance to shuffle his deck too as Vince Lia returned in midfield, while Manny Muscat started at left back after being dropped last week.

The versatile Louis Fenton was then deployed in a wide role up front, despite playing most of the season in defence.

Veteran goalkeeper Glen Moss was also out with a knee injury, which provided an A-League debut for Lewis Italiano.

The 24-year-old Italiano has spent the past two seasons with the Phoenix but had never previously received an opportunity to play.

Things started well for the Phoenix and they won a penalty in the early stages but midfielder Roly Bonevacia pulled his spot kick wide and didn't trouble Sydney custodian Vedran Janjetovic.

Penalties have been an issue for the Phoenix this season as Bonevacia's missed effort was the fifth botched spot kick by the club - in contrast the rest of the league had combined to miss only four this year.

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Minutes later, Bernie Ibini gave Sydney FC the lead with an impressive solo strike and former Phoenix forward Shane Smeltz then gave his old teammates of a reminder of his ability as he converted a penalty in the 32nd minute.

That meant the Phoenix were down 2-0 at halftime, the same situation as last week.

The second spell got underway in perfect fashion for the Phoenix as right back Michael Boxall scored to bring Wellington back in to the contest.

Wellington have been the masters of scoring late goals this season but they were unable to weave any further magic as Sydney held on for a valuable win.

The visitors were able to pack the box well in defence as they retreated in numbers and Wellington were rarely able to catch them on the counter.

Merrick's side will need to provide more when the finals roll around next week.

Sydney FC 2 (Bernie Ibini 14, Shane Smeltz 32 pen) Wellington Phoenix 1 (Michael Boxall 46) halftime: 2-0