Playing their third game in a week, the Wanderers toiled hard on the soggy Pirtek Stadium pitch but couldn't produce the quality to unlock the Reds' defence.
The result all but confirms the Wanderers will lose the Premiers' Plate they won last season to Brisbane Roar, who hold a 10-point advantage with just four games left.
But after bouncing back from last weekend's derby defeat with a midweek win in China, Popovic praised his players' character for producing another solid performance against the Reds.
"Pleased. Very pleased," the Wanderers boss said afterwards.
"Obviously we wanted to win the game and in the end, the second half, we did everything we could to win. We pushed hard.
"(We had) the effort and the character and the desire, in difficult conditions - the pitch was very heavy.
"We probably missed that final pass or the right decision on the edge of the box, because we got there so many times.
"So that's an area we have to improve on. But in the second half we came home strong which was very pleasing."
Popovic used six of the players that only arrived back on Friday from the win over Guizhou Renhe and again opted to rest marquee man Shinji Ono and defender Matthew Spiranovic.
He is hopeful of having the pair back for Wednesday's ACL clash against Kawasaki Frontale.
"We would've liked to have some more fresh legs today, but they weren't ready and we'll have to assess them to see how they are Monday and Tuesday," Popovic said.
Striker Brendon Santalab had a quiet outing in his first appearance since claims he racially abused Sydney FC's Ali Abbas in the derby.
The fall-out and subsequent FFA investigation is sure to have affected Santalab but Popovic said he had no hesitation using the under-fire attacker against the Reds.
"I hadn't seen Brendon all week. I only saw him (on Friday) and he was like everyone else," he said.
"He trained well, he played well today and gave everything he had."
The Wanderers are expected to give a submission to the FFA on Monday in response to Abbas' claims.
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