Keisuke Honda nets Melbourne Victory winner in Big Blue vs. Sydney FC

Keisuke Honda was the match-winner in Melbourne Victory's 2-1 Big Blue triumph over Sydney FC.

Scores were locked at a goal apiece with 20 minutes to go on Sunday after Adam Le Fondre's controversial penalty cancelled Ola Toivonen's opener.

But Van Der Linden then inexplicably took down Honda despite the former Japan international appearing no threat on the by-line.

Honda made no mistake from the penalty spot to net his third goal in his fifth A-League game to lift the Victory into outright second on the table.

"He didn't need to make the challenge in the first place," coach Steve Corica said.

"The ball was almost out. He just had to stay on his feet, not make a foul and things would be fine. But we all make mistakes.

"He'll learn from that, Jop, and we'll get on with it next week."

Played in front of a sellout crowd of 19,081 at Jubilee Stadium, the loss was Sydney FC's first of the season and drops the title contenders to third.

The heaving suburban Sydney venue proved the perfect backdrop for a contest even in possession and opportunity.

Sydney FC controlled the tempo early and could've opened the scoring when Milos Ninkovic's curling effort whizzed past the post.

Instead it was the Victory who cracked the deadlock on Toivonen's 23rd-minute effort after he took full advantage of a James Troisi ball in the box.

Troisi's intended pass for Kosta Barbarouses fell to the Swedish international, who made no mistake in firing it under Andrew Redmayne.

Months after scoring at the World Cup, Toivonen was making his anticipated A-League starting debut having battled an early season calf injury.

But the Sky Blues' frustrations soon turned to relief when referee Peter Green awarded a controversial penalty to the home side in the 33rd minute.

A Ninkovic layoff appeared to have gone past a falling Paul Retre but Green ruled the Sydney winger was nudged by Terry Antonis from behind.

And while replays showed the contact was minimal, it wasn't enough for the video assistant referee to overturn the decision.

And so up stepped Le Fondre, whose penalty was initially saved by Lawrence Thomas, but he reacted quick enough to fire home the rebound.

The former Premier League striker has now scored five goals in as many games but it fell short of preventing Victory claiming their third straight win.

Melbourne coach Kevin Muscat hailed his team for overcoming adversity having faced a similar situation in their derby loss in round one.

"A similar thing happened 4-5 weeks ago in Melbourne, where an incorrect decision went against us and we fell away in that game," he said. "So I was really pleased with the attitude.

"In a moment where something didn't go our way, I thought the second half we were outstanding, the way we accepted it and moved on."