City had a golden chance to go top of the table but were forced to settle for second after failing to capitalise on a dominant performance at AAMI Park on Sunday night.
The Wanderers went ahead in the 19th minute when Jaushua Sotirio scored against the run of play.
Joyce's men drew level through a 54th-minute Ross McCormack penalty but were denied victory by their own poor finishing and a heroic performance from Wanderers goalkeeper Vedran Janjetovic.
It was another frustrating night for Joyce, who felt that City had also deserved better than the 1-0 loss they suffered to defending champions Sydney FC the previous week.
"I didn't think we had a long way to bounce back because I didn't think we were second-best last week against Sydney," Joyce said.
"But likewise tonight we know Western Sydney are a well-established team, a good club with a good coach, so it's not an easy game ... (but) I thought we deserved to win the game.
"I've been in situations where you look back at the end of the season, and hopefully it's a good season for us, where sometimes they're important points as well."
Perhaps the only man more frustrated than Joyce was City striker McCormack.
The Scotland international was involved in everything but struggled to find the back of the net, missing two straightforward headers in quick succession midway through the second half.
Joyce said he expected McCormack and fellow recruits Marcelo Carrusca and Marcin Budzinski to continue to build form and fitness.
"You're getting them up to a level where they have not done pre-season, so it's not like they're battle-hardened and ready to go," he said.
"We're having to introduce them and drip them into the games.
"Ross is starting games but he hadn't done a great deal before he came out here, so there is still more to come from them three."