A blatant refereeing blunder saw reigning A-League champions Sydney FC finally climb off the bottom of the ladder in a controversial 1-0 win over Newcastle at the Sydney Football Stadium on Sunday.

The match appeared doomed for a scoreless draw before Sydney's Brazilian striker Bruno Cazarine broke the deadlock in the 76th minute - but the goal should never have stood.

The Jets were furious after replays showed the ball had crossed the goal line before midfielder Hiro Moriyasu squared it back to allow Cazarine an easy tap-in.

In a bizarre turn of events, assistant referee Ben Wilson had raised his flag for a foul as Moriyasu tussled with Jets defender Nikolai Topor-Stanley just outside the box.

But he soon put his flag down and play was allowed to continue as Moriyasu beat off his opponent, despite the ball appearing to cross the line, with referee Chris Beath awarding the goal despite the Jets' protests.

Newcastle coach Branko Culina was somewhat restrained after the match but clearly frustrated as his side was left languishing at the foot of the table.

"It's part of the game I suppose, hopefully one day we'll get decisions go our way as well," Culina said.

"We've seen that too often those kind of decisions can ruin and determine the outcome of a game.

"I think it should be football rather than those kind of decisions, but having said that if that's what we've got in place, we've just got to accept it."

Topor-Stanley said he stopped when he saw the ball go out but blamed himself for letting Moriyasu get as far as he did.

"It's a bit of a schoolboy error from me, I should have dealt with it before hand and you've got to play the whistle," he said.

Sydney's second win of the season saw them climb over the Jets and North Queensland into ninth spot, as they look to turn the corner after a dismal start to their title defence.

Coach Vitezslav Lavicka admitted the goal was controversial but was relieved some luck had finally fallen his side's way.

"Everyone makes mistakes," Lavicka said.

"We had bad luck this season several times so tonight we had a bit of luck for us."

Cazarine's fifth goal of the season brought to life what had been a miserable match, with both sides justifying their low standing on the ladder.

A dangerous Alex Brosque had Sydney's best chance of the first half while Jets midfielder Ali Abbas should have done better with an unmarked header attempt in the 60th minute.

Newcastle coach Branko Culina took a hard line stance on senior players Ljubo Milicevic and Kasey Wehrman, who both started on the bench after they were involved in an altercation at training on Tuesday.

"We wanted to send a strong message to the players ... and our supporters as well, what we're about and what we want to achieve," Culina said of the decision.