City sat atop the table with four wins heading into Friday night's clash, but the reigning champion Sky Blues leapt into first place with a 1-0 victory at AAMI Park.
Fitzgerald feels City had played well despite the scoreline and is confident of a quick rebound when they take on Western Sydney on Sunday at AAMI Park.
"It's all positive ... I think we were the better team and probably should have got at least a point out of it," Fitzgerald told reporters on Wednesday.
"So we'll take confidence from that ... against arguably the best team in the comp, we can stick with them for most of the game.
"Our defence has been great, we've been a bit unlucky up front and a few things didn't go our way, but that happens in football."
City will take on the Wanderers without superstar striker Tim Cahill, who is with the Socceroos in Honduras.
Western Sydney were held to a frustrating 1-1 draw by 10-man Melbourne Victory on Monday night in Hayden Foxe's last game in charge.
Former Adelaide United coach Josep Gombau will take the reins, with City keeper Eugene Galekovic wary of what his former coach at the Reds will add to his new club.
"It's a strange one because they've got a new coach now and they might change a bit in how they play and their structures," Galekovic said.
"But they've got quality all over the park.
"Whatever they throw at us, we'll be ready.
"In terms of personnel, he might change a few things around and bring players in, but we'll play our own game and we're confident we can do the job."
Fitzgerald and Galekovic, along with W-League players Allanna Kennedy and Lydia Williams, spoke to reporters at Melbourne's Shrine of Remembrance.
Round six of the A-League season is Remembrance Round with players, spectators and officials to honour the sacrifices made by Australia's servicemen and women.
Melbourne City's women's team will take on Newcastle in the early game at AAMI Park.