In the all-Sydney affair, both sides began aggressively, with aggressive defense halting extended periods of possession throughout the opening ten minutes of the match.
The breakthrough came after 11 minutes, as Sydney's marquees combined for the first goal of the match, as Bobo received the ball just outside the box courtesy of a misplaced Mitchell Mallia pass, before crossing to a cutting Filip Holosko who caught the pass on the full and powered the ball into the back of the net past Blacktown keeper Nenad Vekic.
The second came just over ten minutes later, with Bobo playing a role yet again.
Rhyan Grant crossed the ball into the box with the Brazilian heading it onto Dave Carney who connected with a stunning strike from close to 30 yards out in one of the goals of the tournament so far.
New Adelaide United signing Danny Choi looked dangerous at times but while the second period was more closely contested, Sydney FC's full-strength side ultimately proved too strong for Mark Crittenden's resilient squad.
Bobo added his name to the scoresheet as Milos Ninkovic played a ball though for Michael Zullo, setting the striker up for an easy tap-in from less than two yards out for his first goal with his new club 77 minutes into the second half, with the match finishing 3-0 in favour of the A-League side.
In Melbourne, Michael Jakobsen opened the scoring after only two minutes with a back-flip volley from the center of the box, as City looked to continue developing their chemistry in a largely changed but hugely talented squad.
.@Tim_Cahill is on the board for @MelbourneCity. #MagicOfTheCup #MCYvWSW #FFACup pic.twitter.com/7tl29DkK1Q — Westfield FFA Cup (@FFACup) September 21, 2016
Despite questions about how well Tim Cahill and Bruno Fornaroli would fit playing together, the two combined for the second goal of the match at the 32 minute mark, with Cahill providing the assist to last season's A-League Golden Boot.
Australia's leading scorer then opened his account with his new club, scoring a penalty after Nikolai Topor-Stanley was given a red card for taking down Fornaroli in the box as the second half drew to a close.
Fernando Brandan capitalised 20 minutes into the second half, putting the match out of reach of the ten-man Wanderers side who did manage to score a consolation goal courtesy of a Dimas header with the match ending 4-1.
The next quarter-final matches take place on September 27, with Bentleigh Greens playing Melbourne Victory at Kingston Heath while Canberra Olympic host Green Gully at Deakin Reserve.