Marcelo Carrusca and Fabio Ferreria scored in each half to leave the Wanderers without a win in nine matches but coach Tony Popovic said he saw seeds for optimism.
"The boys fought hard, the effort was tremendous," said the former international, who was crowned Asian Football Confederation coach of the year last week following their unlikely Asian Champions League triumph.
"I don't think we can fault some of the football we've been playing, especially our last four games at home, and the way we started today was not a team that lacked confidence.
"The reality is it's nine games without a win, but the player's focus has been there."
Wanderers had goalkeeper Ante Covic to thank for keeping the score respectable after captain Nikolai Topor-Stanley was sent off in the 17th minute following two quick bookings.
Next up for Popovic's side is a showdown with Mexico's Cruz Azul on Saturday at the FIFA Club World Cup in Morocco, though a pay dispute has led to talk of the Wanderers boycotting the lucrative tournament.
In other games, Perth Glory continue to lead the 10-team table after their 2-1 win over Sydney FC on Thursday but they were dealt a blow on Sunday when winger Youssouf Hersi was ruled out for the rest of the campaign because of a hamstring problem.
Melbourne Victory are second, a point behind, after a 3-0 success at Central Coast Mariners, with Adelaide third, two points back of top spot.
Despite the healthy win, Victory boss Kevin Muscat was fuming about the venue switch to the North Sydney Oval.
"For me, football in this country has gone back 20 years tonight. To play on a cricket pitch in this day and age, the steps we have taken forward we have now taken back," he raged.
Rivals Melbourne City, owned by English Premier League champions Manchester City, picked up their first home win of the season by downing Brisbane Roar 1-0 on Sunday to move above the Queenslanders into sixth.
(Writing by Patrick Johnston in Singapore; Editing by Peter Rutherford)
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