Gary van Egmond's side remain bottom of the ladder - three points behind the Central Coast Mariners - after Aziz Behich and Bozhidar Kraev traded second-half goals on Saturday.
The Wanderers have won just two of their last 10 games and are on track to pick up their first-ever wooden spoon, a point underlined by the sparse crowd of just 5081 at CommBank Stadium.
Van Egmond had promised no loyalty in a bid to stop the club's wretched run and the Wanderers' horrendous 4-1 defeat against Sydney FC gave him a mandate to make changes.
Borrello was dropped to the bench for the first time in his Wanderers career after registering just one goal in 12 games.
Van Egmond also turned to a three-man defence which appeared to free up Angus Thurgate and give the Wanderers more threats out wide.
The early signs were encouraging when a shot from Ayman Hammond sailed just wide of Patrick Beach's post before Ryan Fraser and Thurgate had shots blocked.
Hammond went close to grabbing the opener when he charged down Beach after Samuel Soupreyan passed backwards to the unsuspecting City goalkeeper.
City struggled to pose much of a threat to the Wanderers in the first half except for a couple of menacing runs in behind the home side's defence from Marcus Younis.
Aurelio Vidmar's side played with much better intent after halftime but lacked a cutting edge in the final third.
Behich took matters into his own hands soon after van Egmond had thrown Borrello and Kraev into the mix.
The City leftback surged onto a loose ball and drove into the box where he finished past Wanderers goalkeeper Lawrence Thomas in the 65th minute.
The Wanderers pushed forward looking for an equaliser and they found it through Kraev.
The Bulgarian glanced a Thurgate free-kick beyond Beach's reach and into the back of the net in the 77th minute.
Wanderers goalkeeping coach Chris Bowling was sent off in the dying stages after appearing to throw a clipboard.
