The Phoenix looked home and hosed when Ben Sigmund headed home in the 79th minute to add to Tim Brown's opener earlier in the second half.

But a quick-fire double from the increasingly impressive Joel Chianese got the Sky Blues back on equal terms inside four minutes before Paul Ifill ended the visitors' season with a penalty with four minutes to go to book a place in next weekend's minor semi-final against either Perth Glory or Melbourne Heart.

"All season when we've gone behind we've come alive," said a dejected McFlynn.

"We've conceded two goals from set pieces which we pride ourselves on defensively. It was two silly mistakes.

"But all credit to young Joel again. He's a great prospect and has a great future at the club."

But Flynn added: "It (the dressing room) is not a nice place in there at the minute. A defeated dressing room is a very sombre place to be at the best of times, but when your season is over it's hard to look everyone in the eye and know we did enough because ultimately we haven't."

The 3-2 loss was compounded by a calf injury to defender Pascal Bosschaart who was carried from the pitch early in the second half and replaced by Sebastian Ryall.

"It's terrible," said the Dutchman. "I don't know what it is. I felt something crack in my calf. I don't know if it's a bone or a muscle. But it was real, real painful.

"But losing the game is actually the worst thing of all. It couldn't be a worse day."

The defeat not only ended Sydney's season but also brought the curtain down on coach Vitezslav Lavicka's three-year tenure.

Lavicka won the A-League title in his first year in charge in 2009-10 but has been under fire this season after mixed results left Sydney needing to defeat the Newcastle Jets last weekend to even reach the playoffs.

But McFlynn had nothing but praise for his boss.

"Speaking for myself, past players and present players, the club and us as individuals are better people for having known Vitezslav and worked with him," McFlynn said. "I'd like to thank him for three fantastic years at the club."

The Czech coach said the loss meant another chapter in his life had been closed.

"I would like to thank everyone at the club, including the fans, because I've spent a great three years at this club," he said.

"I'm very proud that I was part of a club like Sydney FC. This club will stay in my heart forever."