Wanderers started the brighter of the sides, having had plenty of possession in the early stages of the game.
Jack Earing made a good forward run to create a powerful shot at goal midway through the first half, but the Blues keeper was equal to it as he saved the initial strike.
However, Luca Navarro then followed up the second ball to score a well-crafted header from six yards.
A plethora of chances from Dennis Politic, Joe Pritchard and Marcus Wood came for David Lee's men, but they were unable to extend the lead before the break.
Early into the second half and Birmingham scored an equaliser via a penalty, after McFarlane was brought down in the area and subsquently dispatched the spot kick.
The Whites reacted well going on to create several chances.
The pressure from Wanderers paid dividends, as Navarro and Muscatt combined down the left, before Navarro cut in from the touch line to release Joe Pritchard to score from close range.
Wanderers XI: Aspinall, Brockbank, Muscatt, Edwards (Jones-Griffiths 65), Zouma, Wood, Politic, Earing, Pritchard, Duke-McKenna (King Harmes 75), Navarro